package UpdateCloneAnchors;

=head1 NAME

UpdateCloneAnchors -- Updates the clone anchors in the clone_anchors table so
that differences involved with multiple anchors are resolved.

=head1 SYNOPSIS

UpdateCloneAnchors -> new;

=head1 DESCRIPTION

UpdateCloneAnchors -- Updates the clone anchors in the clone_anchors table so
that differences involved with multiple anchors are resolved.   The updating
is done via a file, ../working_data/clone_anchors.txt, provided by the
user.  This is a tab-delimited text file with the first column being the clone
name, the second column being the anchor, a location, the third column indicates
the index number of a duplicated clone with multiple references, the fourth
column indicates the total number of duplications for a clone, and additional
columns provide more information for the benefit of the user on direct
inspection.

=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()

UpdateCloneAnchors->new;

Updates the clone anchors in the clone_anchors table so that they 
resolve multiple references to anchors.

=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_counted}) {
    message("You must count clone anchors, 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/clone_anchors.txt.");
    my $open_error = FALSE;
    open(INPUT_FILE, "<", "../working_data/clone_anchors.txt")
      or $open_error = TRUE;
    if($open_error) {
      message_start;
      message("Could not open ../working_data/clone_anchors.txt");
      message("$!");
    } # if
    else {
      message("Deleting clone_anchors table for new data");
      $db_manager->execute("delete from clone_anchors");

      message("Obtaining data from clone2locus3 table.");
      my $sth = $db_manager->execute("select clone2locus3.clone, loci.mlg, loci.anchor from clone2locus3, loci, clones where clone2locus3.clone = clones.clone and clones.anchors = 1 and clone2locus3.locus = loci.locus");

      message("Saving the clone2locus data into clone_anchors.");
      my @row = ();
      while(@row = $sth->fetchrow_array()) {
        my $db_eid = $db_manager->{dbh}->quote("");
        my $db_clone = $db_manager->{dbh}->quote(shift @row);
        my $db_mlg = $db_manager->{dbh}->quote(shift @row);
        my $db_anchor = $db_manager->{dbh}->quote(shift @row);
        my $db_dup = $db_manager->{dbh}->quote("1");
        $db_manager->execute("insert into clone_anchors values($db_eid, $db_clone, $db_mlg, $db_anchor, $db_dup, $db_dup)");
      } # while

      message("Getting and saving data from the input file.");
      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++) {
        my $this_line = $file_array[$current_line];
        chomp $this_line;
        my @field_array = split /\t/, $this_line;
        next if($field_array[2] == 0);
        my $db_eid = $db_manager->{dbh}->quote("");
        my $db_clone = $db_manager->{dbh}->quote($field_array[0]);
        my $db_anchor = $db_manager->{dbh}->quote($field_array[1]);
        my $db_dup1 = $db_manager->{dbh}->quote($field_array[2]);
        my $db_dup2 = $db_manager->{dbh}->quote($field_array[3]);
        my $db_mlg = $db_manager->{dbh}->quote($field_array[7]);

        # Save the data in the clone_anchors table
        $db_manager->execute("insert into clone_anchors values($db_eid, $db_clone, $db_mlg, $db_anchor, $db_dup1, $db_dup2)");
      } # for

      close INPUT_FILE;

      $project->{clone_anchors_updated} = TRUE;

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

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