package CrosscheckLocusNames;

=head1 NAME

CrosscheckLocusNames -- Crosschecks the locus names in the clone2locus table with
the locus names in the locus table.

=head1 SYNOPSIS

CrosscheckLocusNames -> new;

=head1 DESCRIPTION

CrosscheckLocusNames -- Crosschecks the locus names in the clone2locus table with
the locus names in the locus table.  Locus names without matches are written
to a bad_locus_names.txt file.

=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()

CrosscheckLocusNames->new;

Crosschecks the locus names in the clone2locus table with the
locus table to determine the ones without matches.

=cut

# package variables

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

sub new {
  my $self = shift;
  my $configuration = shift;
  my $db_manager = shift;
  my $project = shift;

  message_start;
  if($project->{current_project} eq "") {
    message("You must activate a project, first.");
  } # if
  elsif($project->{locus_file} eq "") {
    message("You must read a locus file, first.");
  } # elsif
  elsif($project->{fpc_file} eq "") {
    message("You must read an FPC file, first.");
  } # elsif
  else {
    # The crosscheck can be made
    message("Connecting to the database.");
    $db_manager->connect;

    # Find the loci in clone_loci that match USDA loci
    message("Crosschecking the loci.");
    my $sth = $db_manager->execute("select clone_loci.locus from clone_loci, loci where clone_loci.locus = loci.locus");

    # Read and save the results
    message("Marking the results in clone_loci.");
    my @row = ();
    while(@row = $sth->fetchrow_array()) {
      my $db_locus = $db_manager->{dbh}->quote(shift @row);
      my $db_yes = $db_manager->{dbh}->quote("yes");
      $db_manager->execute("update clone_loci set good = $db_yes where locus = $db_locus");
    } # while

    # Reset update indicator
    $project->{locus_names_updated} = FALSE;

    # Get the bad loci
    my $db_no = $db_manager->{dbh}->quote("no");
    my $sth2 = $db_manager->execute("select locus from clone_loci where good = $db_no");

    # Save the bad loci into a file
    message("Saving bad loci names into bad_loci_names.txt.");
    my $output_error = FALSE;
    open(OUTPUT_FILE, ">", "../working_data/bad_loci_names.txt")
      or $output_error = TRUE;
    if($output_error) {
      message_start;
      message("Could not open ../working_data/bad_loci_names.txt");
      message("$!");
    } # if
    else {
      my @row2 = ();
      while(@row2 = $sth2->fetchrow_array()) {
        my $output_locus = $db_manager->{dbh}->quote(shift @row2);
        $output_locus = substr($output_locus, 1, length($output_locus) - 2);
        print OUTPUT_FILE "$output_locus\n";
      } # while
      $project->{locus_names_crosschecked} = TRUE;
    } # else
    close OUTPUT_FILE;

    message("Disconnecting from the database.");
    $db_manager->disconnect;
  } # else
  press_enter;
} # new

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