package CountContigAnchors;

=head1 NAME

CountContigAnchors -- Counts the number of clone anchors for each
contig and saves the results in the contigs table.

=head1 SYNOPSIS

CountContigAnchors -> new;

=head1 DESCRIPTION

CountContigAnchors -- Counts the number of clone anchors for each
contig and saves the results in the contigs 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()

CountContigAnchors->new;

Counts the number of clone anchors for each contig and saves the
results in the contigs 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->{clone_anchors_updated}) {
    message("You must update clone anchors, first.");
  } # elsif
  else {
    # The counts can be made
    message("Connecting to the database.");
    $db_manager->connect;

    message("Getting the duplicated clones from clone_anchors.");
    my $sth = $db_manager->execute("select clone, dup_t from clone_anchors where dup_t > 1 group by clone");

    message("Saving the duplicate counts to contig2clone.");
    my @row = ();
    while(@row = $sth->fetchrow_array()) {
      my $db_clone = $db_manager->{dbh}->quote(shift @row);
      my $db_dup_t = $db_manager->{dbh}->quote(shift @row);
      $db_manager->execute("update contig2clone set dup_t = $db_dup_t where clone = $db_clone");
    } # while

    $project->{contig_anchors_counted} = TRUE;

    message("Counting the contig anchors.");
    $db_manager->execute("update contigs set anchors = 0");
    my $sth2 = $db_manager->execute("select ctg, sum(contig2clone.dup_t) from contig2clone, clone_anchors where contig2clone.clone = clone_anchors.clone group by ctg");

    message("Saving the counts to contigs.");
    my @row2 = ();
    while(@row2 = $sth2->fetchrow_array()) {
      my $db_ctg = $db_manager->{dbh}->quote(shift @row2);
      my $db_anchors = $db_manager->{dbh}->quote(shift @row2);
      my $db_gamma = $db_manager->{dbh}->quote("gamma");
      $db_manager->execute("update contigs set anchors = $db_anchors, type = $db_gamma where ctg = $db_ctg");
    } # while

    message("Getting contigs with multiple anchors.");
    my $sth3 = $db_manager->execute("select contigs.ctg, clone_anchors.clone, clone_anchors.mlg, clone_anchors.anchor from contig2clone, clone_anchors, contigs where contigs.anchors > 1 and contigs.ctg = contig2clone.ctg and contig2clone.clone = clone_anchors.clone order by contigs.anchors, ctg, mlg, anchor");

    message("Saving the contig information to ../working_data/contig_dups.txt");
    my $output_error = FALSE;
    open (OUTPUT_FILE, ">", "../working_data/contig_dups.txt")
      or $output_error = TRUE;
    if($output_error) {
      message("Could not open ../working/data/contig_dups.txt");
      message("$!");
    } # if
    my @row3 = ();
    while(@row3 = $sth3->fetchrow_array()) {
      my $contig = shift @row3;
      my $clone = shift @row3;
      my $mlg = shift @row3;
      my $anchor = shift @row3;
      if(!$output_error) {
        print OUTPUT_FILE "$contig\t$clone\t$mlg\t$anchor\n";
      } # if
    } # while
    close OUTPUT_FILE;

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

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