package QtlRead;

=head1 NAME

QtlRead -- Read a QTL file and save the pertinent information into the
database

=head1 SYNOPSIS

my $boolean = QtlRead -> new;

=head1 DESCRIPTION

This package reads a QTL file and saves the
pertinent data into the database.  QtlRead, itself,
is not an object and cannot be instantiated.

=head1 VERSION

0.001 (last update:  6/30/04)

=head1 AUTHOR

Chet Langin, clangin@siu.edu

SIU Plant Biotechnology and Genomics Core-facility

=head1 BUGS

None known.

=head1 SEE ALSO

extropy ExtropyConstants ExtropyUtils Extropy::MenuMain

=head1 COPYRIGHT

Copyright 2004, Chet Langin, All Rights Reserved.

This program is free software.  You may copy or
redistribute it under the same terms as Perl itself.

=head1 METHODS

The remainder of this document describes the methods available to the
programmer.

=cut

# load the pragmas
use warnings;
use strict;

# load other modules
use ExtropyConstants;
use ExtropyUtils;

=head2 new()

  my $boolean = QtlRead->new;

Reads a QTL file and loads the data into the database.

=cut

# package variables
my $composite_counter = 0;
my $qtl_locationless_counter = 0;
my $previous_line_blank = 0;
my $qtl_name = "";
my $qtl_counter = 0;
my $gene = "";
my $locus_name = "";
my $locus_counter = 0;
my $start = -1;
my $end = -1;
my $cm_start = -1;
my $cm_end = -1;
my $mlg = "";
my $longest_qtl = 0;
my $zero_length_qtls = 0;
my $shortest_qtl = 100000000;
my $summate_qtl = 0;
my $qtl_divisor = 0;
my $longest_qtl_name = 0;

# ********************************  new  ******************************

sub new {
  my $self = shift;
  my $configuration = shift;
  my $db_manager = shift;
  my $project = shift;
  my $file_name = "";
  my $file_obtained = TRUE;
  my $refresh = FALSE;

  message_start;
  if($project->{current_project} eq "") {
    message("You must activate a project, first.");
    $file_obtained = FALSE;
  } # if
  else {
    # A project has been activated
    if($project->{qtl_file} ne "") {

      message("Data from QTL file $project->{qtl_file}");
      message("is already in the database.");
      if(yes("Refresh the database from this file?")) {
        $file_name = $project->{qtl_file};
        $refresh = TRUE;
      } # if
      elsif(!yes("Delete this existing data in the database and continue?")) {
        return FALSE;
      } # elsif
    } # if
    my $loop = TRUE;
    while($loop) {
      if(!$refresh) {
        message("Give the /path/to/file.txt.");
        blank_line;
        $file_name = prompt("Enter path and QTL file name");
      } # if
      if($file_name eq "Q") {
        $loop = FALSE;
        $file_obtained = FALSE;
      } # if
      elsif(file_name_ok($file_name, $configuration, $db_manager)) {
        $loop = FALSE;
        $file_obtained = TRUE;
      } # elsif
      else {
        $file_obtained = FALSE;
        if(!yes("Try another file name?")) {
          $loop = FALSE;
        } # if
      } # else
    } # while
  } # else(a project has been activated)
  if($file_obtained) {
    # save the configuration
    $project->{qtl_file} = $file_name;
    $configuration->save($project);
    press_enter;
    TRUE;
  } # if
  else {
    press_enter;
    FALSE;
  } # else
} # new
# ********************************  file_name_ok  ******************************

=head2 file_name_ok

  my $boolean = QtlRead->file_name_ok($file_name, $configuration, $db_manager);

Determines if a file name is acceptable.  If the file name is ok, then the QTL file
is read and the data is stored in MySQL for later use.  For internal usage only.

=cut

# ---------------------------------------------------------------------------------
sub file_name_ok {
  my $file_name = shift;
  my $configuration = shift;
  my $db_manager = shift;
  my $name_ok = TRUE;
  my $error = FALSE;
  my $number_lines = 0;
  my $number_qtls = 0;

  open(INPUT_FILE, "<", "$file_name")
    or $error = TRUE;
  if($error) {
    message_start;
    message("Could not read $file_name");
    message("$!");
    $name_ok = FALSE;
  } # if
  else {
    # Read the QTL input file
    message("QTL file $file_name opened");
    message("Connecting to the database.");
    $db_manager->connect;
    message("Deleting previous QTL data in the database.");
    $db_manager->execute("delete from qtl");
    $db_manager->execute("delete from bad_qtl");
    $db_manager->execute("delete from qtl2locus");
    message("Entering data into the database...");

    # read the input file
    my @input_file = <INPUT_FILE>;
    close INPUT_FILE;
    $number_lines = scalar(@input_file);

    # look at each line in the input file
    LINE:for(my $line_counter = 10; $line_counter < $number_lines; $line_counter++) {
      $_ = $input_file[$line_counter];
      chomp; chop;
      if(/^\s*$/){
        # ending a record
        next LINE if($previous_line_blank);
        if($composite_counter == 0) {
          # Save the QTL's in the bad_qtl database table
          my $name_length = length($qtl_name);
          $longest_qtl_name = $name_length if($name_length > $longest_qtl_name);
          my $eid = $db_manager->{dbh}->quote("");
          my $db_qtl = $db_manager->{dbh}->quote("$qtl_name");
          $db_manager->execute("insert into bad_qtl values($eid, $db_qtl)");
          $qtl_locationless_counter++;
        } # if
        elsif($composite_counter != 2) {
          print "Composite counter is not 2:  $line_counter\n";
        } # elsif
        else {
          # this QTL has a location, process it
          # Save the relations in the qtl database table
          my $name_length = length($qtl_name);
          $longest_qtl_name = $name_length if($name_length > $longest_qtl_name);
          my $eid = $db_manager->{dbh}->quote("");
          my $db_qtl = $db_manager->{dbh}->quote("$qtl_name");
          my $db_mlg = $db_manager->{dbh}->quote("$mlg");
          $gene = -1 if($gene eq "");
          my $db_gene = $db_manager->{dbh}->quote("$gene");
          $db_manager->execute("insert into qtl values($eid, $db_qtl, $db_mlg, $cm_start, $cm_end, $start, $end, $db_gene)");
        } # else
        $qtl_name = "";
        $gene = "";
        $composite_counter = 0;
        $previous_line_blank = 1;
        next LINE;
      } # if
      $previous_line_blank = 0;

      my @fields = split / /;
      if($fields[0] eq "QTL") {
        if(!(/^\s*$/, chomp($input_file[$line_counter - 1]))) {
          print "previous line not empty: $line_counter\n";
        } # if
        if($qtl_name ne "") {
          print "Has two QTL fields $line_counter\n";
        } # if
        my @name_fields = split /"/;
        $qtl_name = $name_fields[1];
        $qtl_counter++;
      } # if
      elsif(/^Putative_candidate_gene/) {          # xxx
        my @name_fields = split /"/;
        $gene = $name_fields[1];
      } # elsif
      elsif(/^Candidate_gene/) {          # xxx
        my @name_fields = split /"/;
        $gene = $name_fields[1];
      } # elsif
      elsif(/^Locus/) {
        my @name_fields = split /"/;
        $locus_name = $name_fields[1];
        $locus_counter++;
        if($qtl_name eq "") {
          message("Locus $locus_name has no QTL match.");
        } # if
        else {
          my $eid = $db_manager->{dbh}->quote("");
          my $db_qtl = $db_manager->{dbh}->quote("$qtl_name");
          my $db_locus = $db_manager->{dbh}->quote("$locus_name");
          $db_manager->execute("insert into qtl2locus values($eid, $db_qtl, $db_locus)");
        } # else
      } # elsif
      elsif(/Composite_2/) {
        $composite_counter++;
        if($composite_counter == 1) {
          $fields[-1] = 0 if($fields[-1] < 0);
          $cm_start = $fields[-1];
          $start = sprintf("%08.0f", $fields[-1] * FACTOR);
          # get the MLG
          my @fields = split /"/;
          # I added the below condition because not all of the entries have quote marks
          if(!$fields[1]) {
            @fields = split / /;
          } # if
          my $mlg_field = $fields[1];
          my @mlg_sub_fields = split /-/, $mlg_field;
          $mlg = uc $mlg_sub_fields[0];
          if(/(A1|A2|B1|B2|C1|C2|D1A|D1B|D2|E|F|G|H|I|J|K|L|M|N|O)/, $mlg) {
            # (nothing)
          } # if
          else {
            message("MLG $mlg not recognized.");
          } # else
          $mlg = "D1AQ" if($mlg eq "D1A");
          $mlg = "D1BW" if($mlg eq "D1B");
        } # if
        else {
          # composite_counter != 1 (it equals 2)
          $cm_end = $fields[-1];
          $end = sprintf("%08.0f", $fields[-1] * FACTOR);
          $longest_qtl = $end - $start if(($end - $start) > $longest_qtl);
          if($end - $start == 0) {
            $zero_length_qtls++;
            print "zero-length QTL:  $qtl_name\n";
          } # if
          else {
            $shortest_qtl = $end - $start if(($end - $start) < $shortest_qtl);
          } # else
          $summate_qtl += $end - $start;
          $qtl_divisor++;
        } # else
      } # elsif
    } # for

    # print closing information
    message("QTL's:  $qtl_counter ($qtl_locationless_counter have no locations given).");
    message("Longest QTL:  $longest_qtl.");
    message("Shortest QTL:  $shortest_qtl.");
    my $average = $summate_qtl / $qtl_divisor;
    message("Average QTL:  $average.");
    message("Zero-length QTL's:  $zero_length_qtls.");
    message("Longest QTL name:  $longest_qtl_name.");
    message("QTL/Locus relations:  $locus_counter.");
  } # else

  message("Disconnecting from the database.");
  $db_manager->disconnect;
  close INPUT_FILE;

  if($name_ok) {
    TRUE;
  } # if
  else {
    FALSE;
  } # else
} # project_name_ok

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