package RelRead;

=head1 NAME

RelRead -- Read a Related Genes file and save the pertinent information into the
database

=head1 SYNOPSIS

my $boolean = RelRead -> new;

=head1 DESCRIPTION

This package reads a Related Genes file and saves the
pertinent data into the database.  RelRead, itself,
is not an object and cannot be instantiated.

=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()

  my $boolean = RelRead->new;

Reads a Related Genes file and loads the data into the database.

=cut

# package variables

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

sub new {
  my $self = shift;
  my $configuration = shift;
  my $db_manager = shift;
  my $project = shift;
  my $file_name = "";
  my $file_obtained = TRUE;
  my $refresh = FALSE;

  message_start;
  if($project->{current_project} eq "") {
    message("You must activate a project, first.");
    $file_obtained = FALSE;
  } # if
  else {
    # A project has been activated
    if($project->{rel_file} ne "") {
      message("Data from Related Genes file $project->{rel_file}");
      message("is already in the database.");
      if(yes("Refresh the database from this file?")) {
        $file_name = $project->{rel_file};
        $refresh = TRUE;
      } # if
      elsif(!yes("Delete this existing data in the database and continue?")) {
        return FALSE;
      } # elsif
    } # if
    my $loop = TRUE;
    while($loop) {
      if(!$refresh) {
        message("Give the /path/to/file.txt.");
        blank_line;
        $file_name = prompt("Enter path and Related Genes file name");
      } # if
      if($file_name eq "Q") {
        $loop = FALSE;
        $file_obtained = FALSE;
      } # if
      elsif(file_name_ok($file_name, $configuration, $db_manager)) {
        $loop = FALSE;
        $file_obtained = TRUE;
      } # elsif
      else {
        $file_obtained = FALSE;
        if(!yes("Try another file name?")) {
          $loop = FALSE;
        } # if
      } # else
    } # while
  } # else(a project has been activated)
  if($file_obtained) {
    # save the configuration
    $project->{rel_file} = $file_name;
    $configuration->save($project);
    press_enter;
    TRUE;
  } # if
  else {
    press_enter;
    FALSE;
  } # else
} # new
# ********************************  file_name_ok  ******************************

=head2 file_name_ok

  my $boolean = RelRead->file_name_ok($file_name, $configuration, $db_manager);

Determines if a file name is acceptable.  If the file name is ok, then the Related
Genes file is read and the data is stored in MySQL for later use.  For internal
usage only.

=cut

# ---------------------------------------------------------------------------------
sub file_name_ok {
  my $file_name = shift;
  my $configuration = shift;
  my $db_manager = shift;
  my $name_ok = TRUE;
  my $error = FALSE;
  my $number_lines = 0;

  open(INPUT_FILE, "<", "$file_name")
    or $error = TRUE;
  if($error) {
    message_start;
    message("Could not read $file_name");
    message("$!");
    $name_ok = FALSE;
  } # if
  else {
    # Read the Related Genes input file
    message("Related Genes file $file_name opened");
    message("Connecting to the database.");
    $db_manager->connect;
    message("Deleting any previous Related Genes data in the database.");
    $db_manager->execute("delete from related");
    message("Entering data into the database...");

    # read the input file
    my @file_array = <INPUT_FILE>;
    close INPUT_FILE;
    $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 @field_array = split /\t/, $file_array[$current_line];
      my $mlg = $field_array[0];
      my $start = $field_array[3];
      my $end = $field_array[4];
      my $data_field = $field_array[8];
      my @data_array = split /"/, $data_field;
      my $related = $data_array[1];
      my $hit = $data_array[3];

      # Save the relations in the related database table
      $related = $db_manager->{dbh}->quote($related);
      $db_manager->execute("insert into related values('', $related, '$hit', '$mlg', '$start', '$end')");
    } # for

    # print closing information
    message("Number of Related Genes:  $number_lines");
  } # else

  message("Disconnecting from the database.");
  $db_manager->disconnect;
  close INPUT_FILE;

  if($name_ok) {
    TRUE;
  } # if
  else {
    FALSE;
  } # else
} # file_name_ok

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