package CountCloneAnchors;

=head1 NAME

CountCloneAnchors -- Counts the number of locus anchors for each
clone and saves the results in the clones table.

=head1 SYNOPSIS

CountCloneAnchors -> new;

=head1 DESCRIPTION

CountCloneAnchors -- Counts the number of locus anchors for each
clone and saves the results in the clones table.

=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

The module is under development and is not yet finished.

=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()

CountCloneAnchors->new;

Counts the number of locus anchors for each clone and saves the
results in the clones 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($project->{current_project} eq "") {
    message("You must activate a project, first.");
    blank_line;
    press_enter;
  } # if
  elsif(!$project->{locus_names_updated}) {
    message("You must update locus names, first.");
    blank_line;
    press_enter;
  } # elsif
  else {
    # The counts can be made
    message("Connecting to the database.");
    $db_manager->connect;

    message("Clearing the counts in the clones table.");
    $db_manager->execute("update clones set anchors = 0");

    message("Counting the anchors.");
    my $sth = $db_manager->execute("select count(clone), clone from clone2locus3 group by clone");

    message("Saving the counts to the clones table.");
    my @row = ();
    while(@row = $sth->fetchrow_array()) {
      my $db_count = $db_manager->{dbh}->quote(shift @row);
      my $db_clone = $db_manager->{dbh}->quote(shift @row);
      $db_manager->execute("update clones set anchors = $db_count where clone = $db_clone");
    } # while
    $project->{clone_anchors_counted} = TRUE;

    message("Finding the clones with more than one anchor.");
    my $sth2 = $db_manager->execute("select clones.clone, clones.anchors, clone2locus3.locus, clone2locus3.mlg, loci.mlg, loci.anchor from clones, clone2locus3, loci where clones.anchors > 1 and clones.clone = clone2locus3.clone and clone2locus3.locus = loci.locus order by clones.anchors, clones.clone");

    message("Saving the clone information to ../working_data/clone_dups.txt");
    my $output_error = FALSE;
    open (OUTPUT_FILE, ">", "../working_data/clone_dups.txt")
      or $output_error = TRUE;
    if($output_error) {
      message("Could not open ../working/data/clone_dups.txt");
      message("$!");
    } # if
    my @row2 = ();
    while(@row2 = $sth2->fetchrow_array()) {
      my $clone = shift @row2;
      my $anchors = shift @row2;
      my $locus = shift @row2;
      my $mlg1 = shift @row2;
      my $mlg2 = shift @row2;
      my $anchor = shift @row2;
      if(!$output_error) {
        print OUTPUT_FILE "$clone\t$anchors\t$locus\t$mlg1\t$mlg2\t$anchor\n";
      } # if
    } # while
    close OUTPUT_FILE;

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

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