#!/opt/conda/conda-bld/meme_1618213960901/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/bin/perl

=head1 NAME

mast_xml_to_html - Make a MAST HTML output from a MAST XML output.

=head1 SYNOPSIS

mast_xml_to_html <MAST XML file> <MAST HTML file>
=cut

use strict;
use warnings;

use Cwd qw(abs_path);
use Fcntl qw(O_RDONLY SEEK_SET);
use File::Basename qw(fileparse);
use File::Spec::Functions qw(tmpdir);
use File::Temp qw(tempfile);
use Getopt::Long;
use Pod::Usage;
use XML::Parser::Expat;

use lib '/opt/conda/conda-bld/meme_1618213960901/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib/meme-5.3.0/perl';

my $etc_dir;
my $temp_dir;
my $scripts_dir;

#
# initialise the global constants
# 
sub initialise {
  # setup etc dir
  $etc_dir = defined($ENV{MEME_DATA_DIR}) ? $ENV{MEME_DATA_DIR} : '/opt/conda/conda-bld/meme_1618213960901/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/share/meme-5.3.0';
  # setup temporary directory
  $temp_dir = '';
  # use the perl default if none is supplied or the replace fails
  $temp_dir = tmpdir() if ($temp_dir eq '' || $temp_dir =~ m/^\@TMP[_]DIR\@$/);

  # find the location of the script
  my $script_name;
  ($script_name, $scripts_dir) = fileparse(__FILE__);
  $scripts_dir = abs_path($scripts_dir);

  # add script location to search path
  unshift(@INC, $scripts_dir);

  require HtmlMonolithWr;
  require MastSAX;
}

sub arguments {
  # Set Option Defaults
  my $options = {XML_PATH => undef, HTML_PATH => undef};
  # General Options
  my $help = 0; # FALSE
  my @errors = ();
  my @dbs = ();

  # get the options from the arguments
  my $options_success = 0; # FALSE
  # redirect stderr to a temp file so we can get the error message from GetOptions
  my $olderr;
  my $tmperr = tempfile('GetOptions_XXXXXXXXXX', DIR => $temp_dir, UNLINK => 1);
  open($olderr, ">&STDERR") or die("Can't dup STDERR: $!");
  open(STDERR, '>&', $tmperr) or die("Can't redirect STDERR to temp file: $!");
  # parse options
  $options_success = GetOptions(
    'help|?'          => \$help,
  );
  ($options->{XML_PATH}, $options->{HTML_PATH}) = @ARGV;
  # display help
  pod2usage(1) if $help;
  # reset STDERR
  open(STDERR, ">&", $olderr) or die("Can't reset STDERR: $!");
  # read argument parsing errors
  seek($tmperr, 0, SEEK_SET);
  while (<$tmperr>) {chomp; push(@errors, $_);}
  close($tmperr);
  # check source XML file
  unless (defined($options->{XML_PATH})) {
    push(@errors, "No MAST XML file specified");
  } elsif (not -e $options->{XML_PATH}) {
    push(@errors, "The MAST XML file specified does not exist");
  }
  unless (defined($options->{HTML_PATH})) {
    push(@errors, "No output file specified");
  }
  # print errors
  foreach my $error (@errors) {
    print STDERR $error, "\n";
  }
  pod2usage(2) if @errors;
  # return options
  return $options;
}

sub _start_mast {
  my ($info, $version, $release) = @_;
  my $wr = $info->{wr};
  $wr->str_prop('program', 'MAST');
  $wr->str_prop('version', $version);
  $wr->str_prop('release', $release);
}

sub _handle_command_line {
  my ($info, @args) = @_;
  my $wr = $info->{wr};
  $wr->str_array_prop("cmd", @args);
}

sub _handle_settings {
  my ($info, $strand_handling, $max_correlation, $remove_correlated,
    $max_seq_evalue, $adjust_hit, $max_hit_pvalue, $max_weak_pvalue) = @_;
  my $wr = $info->{wr};
  $wr->property("settings");
  $wr->start_object_value();
  $wr->str_prop("strand_handling", $strand_handling);
  $wr->num_prop("max_correlation", $max_correlation);
  $wr->bool_prop("remove_correlated", $remove_correlated);
  $wr->num_prop("max_seq_evalue", $max_seq_evalue);
  $wr->bool_prop("adjust_hit", $adjust_hit);
  $wr->num_prop("max_hit_pvalue", $max_hit_pvalue);
  $wr->num_prop("max_weak_pvalue", $max_weak_pvalue);
  $wr->end_object_value();
}

sub _handle_alphabet {
  my ($info, $alph) = @_;
  my $wr = $info->{wr};
  $wr->property("alphabet");
  $alph->to_json($wr);
}

sub _handle_sequence_alphabet {
  my ($info, $seq_alph) = @_;
  my $wr = $info->{wr};
  $wr->property("sequence_alphabet");
  $seq_alph->to_json($wr);
}

sub _handle_translate {
  my ($info, $num_seq, $num_mot) = @_;
  my $wr = $info->{wr};
  $wr->num_prop("xlate", $num_seq);
}

sub _handle_background {
  my ($info, $from, @probs) = @_;
  my $wr = $info->{wr};
  $wr->property("background");
  $wr->start_object_value();
  $wr->str_prop("source", $from);
  $wr->num_array_prop("freqs", @probs);
  $wr->end_object_value();
}

sub _start_motif_dbs {
  my ($info) = @_;
  my $wr = $info->{wr};
  $wr->property("motif_dbs");
  $wr->start_array_value();
}

sub _handle_motif_db {
  my ($info, $source, $name, $last_mod_date, $bg) = @_;
  my $wr = $info->{wr};
  $wr->start_object_value();
  $wr->str_prop("source", $source);
  $wr->str_prop("name", $name) if defined $name;
  $wr->str_prop("last_mod_date", $last_mod_date);
  $wr->num_array_prop("bg", @{$bg});
  $wr->end_object_value();
}

sub _end_motif_dbs {
  my ($info) = @_;
  my $wr = $info->{wr};
  $wr->end_array_value();
}

sub _start_motifs {
  my ($info) = @_;
  my $wr = $info->{wr};
  $wr->property("motifs");
  $wr->start_array_value();
}

sub _handle_motif {
  my ($info, $db, $id, $alt, $len, $nsites, $evalue, $bad, $url, $psm) = @_;
  $info->{nmotifs} += 1;
  my $wr = $info->{wr};
  $wr->start_object_value();
  $wr->num_prop("db", $db);
  $wr->str_prop("id", $id);
  $wr->str_prop("alt", $alt) if (defined($alt));
  $wr->num_prop("len", $len);
  $wr->num_prop("nsites", $nsites) if (defined($nsites));
  $wr->str_prop("evalue", $evalue) if (defined($evalue));
  $wr->bool_prop("bad", $bad) if (defined($bad));
  $wr->str_prop("url", $url) if $url;
  $wr->property("psm");
  $wr->start_array_value();
  for (my $i = 0; $i < scalar(@{$psm}); $i++) {
    $wr->num_array_value(@{$psm->[$i]});
  }
  $wr->end_array_value();
  $wr->end_object_value();
}

sub _end_motifs {
  my ($info) = @_;
  my $wr = $info->{wr};
  $wr->end_array_value();
}

sub _start_correlations {
  my ($info) = @_;
}

sub _handle_correlation {
  my ($info, $idx_a, $idx_b, $value) = @_;
  my $set = $info->{correlations};
  $set->{$idx_a} = {} unless defined $set->{$idx_a};
  $set->{$idx_a}->{$idx_b} = $value;
}

sub _end_correlations {
  my ($info) = @_;
  my $wr = $info->{wr};
  my $nmotifs = $info->{nmotifs};
  my $set = $info->{correlations};
  $wr->property("correlation");
  $wr->start_array_value();
  for (my $i = 0; $i < $nmotifs; $i++) {
    $wr->start_array_value();
    for (my $j = 0; $j < $nmotifs; $j++) {
      if ($i == $j) {
        $wr->null_value();
      } else {
        my $value = ($j < $i ? $set->{$j}->{$i} : $set->{$i}->{$j});
        print "i: $i, j: $j\n" unless defined $value;
        $wr->num_value($value);
      }
    }
    $wr->end_array_value();
  }
  $wr->end_array_value();
}

sub _start_nos {
  my ($info) = @_;
  my $wr = $info->{wr};
  $wr->property("nos");
  $wr->start_array_value();
}

sub _handle_expect {
  my ($info, $gap, $idx) = @_;
  my $wr = $info->{wr};
  $wr->start_object_value();
  $wr->num_prop("gap", $gap) if defined $gap;
  $wr->num_prop("idx", $idx);
  $wr->end_object_value();
}

sub _end_nos {
  my ($info) = @_;
  my $wr = $info->{wr};
  $wr->end_array_value();
}

sub _start_sequence_dbs {
  my ($info) = @_;
  my $wr = $info->{wr};
  $wr->property("sequence_dbs");
  $wr->start_array_value();
}

sub _handle_sequence_db {
  my ($info, $source, $name, $last_mod_date, $sequence_count, $residue_count, $link) = @_;
  my $wr = $info->{wr};
  $wr->start_object_value();
  $wr->str_prop("source", $source);
  $wr->str_prop("name", $name) if defined $name;
  $wr->str_prop("last_mod_date", $last_mod_date);
  $wr->num_prop("sequence_count", $sequence_count);
  $wr->num_prop("residue_count", $residue_count);
  $wr->str_prop("link", $link) if defined $link;
  $wr->end_object_value();
}

sub _end_sequence_dbs {
  my ($info) = @_;
  my $wr = $info->{wr};
  $wr->end_array_value();
}

sub _start_sequences {
  my ($info) = @_;
  my $wr = $info->{wr};
  $wr->property("sequences");
  $wr->start_array_value();
}

sub _start_sequence {
  my ($info, $db, $name, $comment, $length) = @_;
  $info->{scores} = []; # False
  $info->{first_seg} = 1; # True
  my $wr = $info->{wr};
  $wr->start_object_value();
  $wr->num_prop("db", $db);
  $wr->str_prop("name", $name);
  $wr->str_prop("comment", $comment) if defined $comment;
  $wr->num_prop("length", $length);
}

sub _handle_score {
  my ($info, $strand, $combined_pvalue, $evalue, $frame) = @_;
  my $pos = ($strand eq 'both' || $strand eq 'forward' ? 0 : 1);
  while (scalar(@{$info->{scores}}) < $pos) {
    push(@{$info->{scores}}, undef);
  }
  $info->{scores}->[$pos] = {
    combined_pvalue => $combined_pvalue,
    evalue => $evalue,
    frame => $frame
  };
}

sub _write_scores {
  my ($info) = @_;
  my $wr = $info->{wr};
  $wr->property("score");
  $wr->start_array_value();
  for (my $i = 0; $i < scalar(@{$info->{scores}}); $i++) {
    my $score = $info->{scores}->[$i];
    if (defined($score)) {
      $wr->start_object_value();
      $wr->num_prop("combined_pvalue", $score->{combined_pvalue});
      $wr->num_prop("evalue", $score->{evalue});
      $wr->str_prop("frame", $score->{frame}) if (defined($score->{frame}));
      $wr->end_object_value();
    } else {
      $wr->null_value();
    }
  }
  $wr->end_array_value();
}

sub _start_seg {
  my ($info, $start_pos) = @_;
  my $wr = $info->{wr};
  if ($info->{first_seg}) {
    &_write_scores($info);
    $wr->property("segs");
    $wr->start_array_value();
    $info->{first_seg} = 0; # False
  }
  $wr->start_object_value();
  $wr->num_prop("pos", $start_pos - 1); # change to zero indexed
}

sub _handle_data {
  my ($info, $sequence) = @_;
  my $wr = $info->{wr};
  $wr->str_prop("data", $sequence);
  $wr->property("hits");
  $wr->start_array_value();
}

sub _handle_hit {
  my ($info, $pos, $idx, $rc, $pvalue, $match, $translation) = @_;
  my $wr = $info->{wr};
  $wr->start_object_value();
  $wr->num_prop("pos", $pos  - 1); # change to zero indexed
  $wr->num_prop("idx", $idx);
  $wr->bool_prop("rc", $rc);
  $wr->num_prop("pvalue", $pvalue);
  $wr->str_prop("match", $match);
  $wr->str_prop("translation", $translation) if defined $translation;
  $wr->end_object_value();
}

sub _end_seg {
  my ($info) = @_;
  my $wr = $info->{wr};
  $wr->end_array_value();
  $wr->end_object_value();
}

sub _end_sequence {
  my ($info) = @_;
  my $wr = $info->{wr};
  if ($info->{first_seg}) {
    &_write_scores($info);
  } else {
    $wr->end_array_value();
  }
  $wr->end_object_value();
}

sub _end_sequences {
  my ($info) = @_;
  my $wr = $info->{wr};
  $wr->end_array_value();
}

sub _handle_runtime {
  my ($info, $host, $when, $cycles, $seconds) = @_;
  my $wr = $info->{wr};
  $wr->property("runtime");
  $wr->start_object_value();
  $wr->str_prop("host", $host);
  $wr->str_prop("when", $when);
  $wr->num_prop("cycles", $cycles);
  $wr->num_prop("seconds", $seconds);
  $wr->end_object_value();
}

sub _end_mast {
  my ($info) = @_;

}

sub transform_data {
  my ($opts, $jsonwr) = @_;
  my $info = {wr => $jsonwr, correlations => {}, nmotifs => 0};

  my $sax = new MastSAX($info,
    start_mast => \&_start_mast,
    handle_command_line => \&_handle_command_line,
    handle_settings => \&_handle_settings,
    handle_alphabet => \&_handle_alphabet,
    handle_sequence_alphabet => \&_handle_sequence_alphabet,
    handle_translate => \&_handle_translate,
    handle_background => \&_handle_background,
    start_motif_dbs => \&_start_motif_dbs,
    handle_motif_db => \&_handle_motif_db,
    end_motif_dbs => \&_end_motif_dbs,
    start_motifs => \&_start_motifs,
    handle_motif => \&_handle_motif,
    end_motifs => \&_end_motifs,
    start_correlations => \&_start_correlations,
    handle_correlation => \&_handle_correlation,
    end_correlations => \&_end_correlations,
    start_nos => \&_start_nos,
    handle_expect => \&_handle_expect,
    end_nos => \&_end_nos,
    start_sequence_dbs => \&_start_sequence_dbs,
    handle_sequence_db => \&_handle_sequence_db,
    end_sequence_dbs => \&_end_sequence_dbs,
    start_sequences => \&_start_sequences,
    start_sequence => \&_start_sequence,
    handle_score => \&_handle_score,
    start_seg => \&_start_seg,
    handle_data => \&_handle_data,
    handle_hit => \&_handle_hit,
    end_seg => \&_end_seg,
    end_sequence => \&_end_sequence,
    end_sequences => \&_end_sequences,
    handle_runtime => \&_handle_runtime,
    end_mast => \&_end_mast
  );
  my $fh;
  sysopen($fh, $opts->{XML_PATH}, O_RDONLY) or die("Failed to open file \"$opts->{XML_PATH}\"\n");
  while (<$fh>) {
    $sax->parse_more($_);
    if ($sax->has_errors()) {
      die("Failed to write HTML output due to errors processing the XML:\n" . join("\n", $sax->get_errors()));
    }
  }
  $sax->parse_done();
  if ($sax->has_errors()) {
    die("Failed to write HTML output due to errors processing the XML:\n" . join("\n", $sax->get_errors()));
  }  
}

sub main {
  &initialise();
  my $opts = &arguments();
  # start writing HTML
  my $htmlwr = new HtmlMonolithWr($etc_dir, 'mast_template.html',  $opts->{HTML_PATH}, 'mast_data.js' => 'data');
  # transform the XML into JSON
  &transform_data($opts, $htmlwr->output());
  # finish writing HTML
  $htmlwr->output();
}

&main();
1;

