package UpdateLocusNames;

=head1 NAME

UpdateLocusNames -- Updates the locus names in the clone2locus table so
that they match locus names in the locus table.

=head1 SYNOPSIS

UpdateLocusNames -> new;

=head1 DESCRIPTION

UpdateLocusNames -- Updates the locus names in the clone2locus table so
that they matche locus names in the locus table.  The updating is done
via a file, ../working_data/locus_name_changes.txt, provided by the
user.  This is a two-column tab-delimited text file with the first
column being the old locus name and the second column being the 
corresponding new locus name.

=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()

UpdateLocusNames->new;

Updates the locus names in the clone2locus table so that they 
match locus names in the loci table.

=cut

# package variables

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

sub new {
  my $self = shift;
  my $configuration = shift;
  my $db_manager = shift;
  my $project = shift;
  my $number_lines = 0;

  message_start;
  if($project->{current_project} eq "") {
    message("You must activate a project, first.");
  } # if
  elsif(!$project->{locus_names_crosschecked}) {
    message("You must crosscheck locus names, first.");
  } # elsif
  else {
    # The updates can be made
    message("Connecting to the database.");
    $db_manager->connect;

    # Open and read the update file
    message("Opening ../working_data/locus_name_changes.txt.");
    my $open_error = FALSE;
    open(INPUT_FILE, "<", "../working_data/locus_name_changes.txt")
      or $open_error = TRUE;
    if($open_error) {
      message_start;
      message("Could not open ../working_data/locus_name_changes.txt");
      message("$!");
    } # if
    else {
      message("Making locus name changes to clone2locus2 table.");

      # Deleting clone2locus2 for new data
      message("Deleting clone2locus2 for new data");
      $db_manager->execute("delete from clone2locus2");

      # Copy clone2locus data to clone2locus2
      message("Copying clone2locus data to clone2locus2");
      $db_manager->execute("insert into clone2locus2 select * from clone2locus");

      my @file_array = <INPUT_FILE>;
      close INPUT_FILE;
      my $number_lines = scalar(@file_array);

      # look at each line in the input file
      for(my $current_line=0; $current_line < $number_lines; $current_line++) {
        # Get a name change
        my $this_line = $file_array[$current_line];
        chomp $this_line;
        my @field_array = split /\t/, $this_line;
        my $old_name = $db_manager->{dbh}->quote($field_array[0]);
        my $new_name = $db_manager->{dbh}->quote($field_array[1]);

        # Save the name change in the clone2locus2 table
        my $handle = $db_manager->execute("update clone2locus2 set locus = $new_name where locus = $old_name");
        my $rows = $handle->rows;
        # print "$rows ";
      } # for

      # Deleting clone_loci2 for new data
      message("Deleting clone_loci2 for new data");
      $db_manager->execute("delete from clone_loci2");

      # Get the new clone names from clone2loci;
      message("Getting the new locus names from clone2locus.");
      my $sth = $db_manager->execute("select locus from clone2locus2");

      # Read and save the results
      message("Saving the new locus names in clone_loci2.");
      my @row = ();
      while(@row = $sth->fetchrow_array()) {
        my $eid = $db_manager->{dbh}->quote("");
        my $db_locus = $db_manager->{dbh}->quote(shift @row);
        my $db_no = $db_manager->{dbh}->quote("no");
        $db_manager->execute("insert into clone_loci2 values($eid, $db_locus, $db_no)");
      } # while

      # Find the loci in clone_loci2 that match USDA loci
      message("Crosschecking the new loci.");
      my $sth2 = $db_manager->execute("select clone_loci2.locus from clone_loci2, loci where clone_loci2.locus = loci.locus");

      # Read and save the results
      message("Marking the results in clone_loci2.");
      my @row2 = ();
      while(@row2 = $sth2->fetchrow_array()) {
        my $db_locus = $db_manager->{dbh}->quote(shift @row2);
        my $db_yes = $db_manager->{dbh}->quote("yes");
        $db_manager->execute("update clone_loci2 set good = $db_yes where locus = $db_locus");
      } # while

      # Find the loci names that are still bad
      my $db_no = $db_manager->{dbh}->quote("no");
      my $sth3 = $db_manager->execute("select locus from clone_loci2 where good = $db_no");

      # Processing loci that still have bad names
      message("Deleting clone2locus3 table data to accomodate new data");
      $db_manager->execute("delete from clone2locus3");
      message("Deleting bad_clone2locus table data to accomodate new data");
      $db_manager->execute("delete from bad_clone2locus");
      message("Saving bad loci names into bad_loci_names2.txt,");
      message("and rearranging table data to reflect bad loci names.");
      my $output_error = FALSE;
      open(OUTPUT_FILE, ">", "../working_data/bad_loci_names2.txt")
        or $output_error = TRUE;
      if($output_error) {
        message_start;
        message("Could not open ../working/data/bad_loci_names2.txt");
        message("$!");
      } # if
      else {
        # output file has been successfully opened
        my @row3 = ();
        while(@row3 = $sth3->fetchrow_array()) {
          my $output_locus = $db_manager->{dbh}->quote(shift @row3);
          my $db_no = $db_manager->{dbh}->quote("no");
          my $db_yes = $db_manager->{dbh}->quote("yes");
          my $db_locus = $output_locus;
          $output_locus = substr($output_locus, 1, length($output_locus) - 2);
          print OUTPUT_FILE "$output_locus\n";
          $db_manager->execute("insert into bad_clone2locus select clone2locus2.eid, clone2locus2.clone, clone2locus2.locus, clone2locus2.mlg from clone2locus2, clone_loci2 where clone2locus2.locus = clone_loci2.locus and clone_loci2.good = $db_no");
          $db_manager->execute("insert into clone2locus3 select clone2locus2.eid, clone2locus2.clone, clone2locus2.locus, clone2locus2.mlg from clone2locus2, clone_loci2 where clone2locus2.locus = clone_loci2.locus and clone_loci2.good = $db_yes");
        } # while

        $project->{locus_names_updated} = TRUE;
      } # else
      close OUTPUT_FILE;

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

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