package ConRead;

=head1 NAME

ConRead -- Read a Confirmed file and save the pertinent information into the
database

=head1 SYNOPSIS

my $boolean = ConRead -> new;

=head1 DESCRIPTION

This package reads a Confirmedfile and saves the
pertinent data into the database.  ConRead, 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 = ConRead->new;

Reads a Confirmed 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->{con_file} ne "") {
      message("Data from Confirmed file $project->{con_file}");
      message("is already in the database.");
      if(yes("Refresh the database from this file?")) {
        $file_name = $project->{con_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;
        $file_name = prompt("Enter path and Confirmed file name");
      } # if
      if($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->{con_file} = $file_name;
    $configuration->save($project);
    press_enter;
    TRUE;
  } # if
  else {
    press_enter;
    FALSE;
  } # else
} # new
# ********************************  file_name_ok  ******************************

=head2 file_name_ok

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

Determines if a file name is acceptable.  If the file name is ok, then the Confirmed
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 $output_error = FALSE;
  my $number_lines = 0;

  open(INPUT_FILE, "<", "$file_name")
    or $error = TRUE;
  if($error) {
    message("Could not read $file_name");
    message("$!");
    $name_ok = FALSE;
  } # if

  open(OUTPUT_FILE, ">", "../given_data/iastate_loci.txt")
    or $output_error = FALSE;
  if($output_error == TRUE) {
    message("Could not open output file");
    message("$!");
  } # if

  else {
    # Read the Confirmed input file
    message("Confirmed file $file_name opened");
    message("Connecting to the database.");
    $db_manager->connect;
    message("Deleting any previous Confirmed data in the database.");
    $db_manager->execute("delete from confirmed");
    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 $this_line = $file_array[$current_line];
      chomp $this_line;
      my @field_array = split /\t/, $this_line;
      my $probe = $field_array[0];
      my $probe2 = $field_array[1];
      my $clone = $field_array[2];
      my $mlg = $field_array[3];
      my $cM = $field_array[4];
      my $method = $field_array[5];

      $probe2 =~ s/^Gm_//;
      $probe2 =~ s/_ctg_.$//;

      $clone =~ s/^Gm_//;
      $clone =~ s/b001//;
      $clone =~ s/_//g;

      $cM = "-1" if($cM eq "");

      $method =~ s/\s$//;
      if($method =~ /RFLP-1/) {
        $method = "RFLP-1 soybase locus";
      } # if
      if($method =~ /RFLP-2/) {
        $method = "RFLP-2 soybase locus";
      } # if
      if($method =~ /RFLP-3/) {
        $method = "RFLP-3 soybase locus";
      } # if

      # Save the relations in the confirmed database table
      $db_manager->execute("insert into confirmed values('', '$probe', '$probe2', '$clone', '$mlg', '$cM', '$method')");

      # write to iastate.txt file, if appropriate
      if($cM != -1) {
        my $sth1 = $db_manager->execute("select locus from loci where locus = 'probe'");
        my @row1 = ();
        my $found = FALSE;
        while(@row1 = $sth1->fetchrow_array()) {
          $found = TRUE;
        } # while
        if($found == FALSE) {
          print OUTPUT_FILE "$probe\t$mlg\t$cM\tIAState\tIAState\n";
        } # if
        if($probe ne $probe2) {
          my $sth2 = $db_manager->execute("select locus from loci where locus = 'probe2'");
          my @row2 = ();
          my $found = FALSE;
          while(@row2 = $sth2->fetchrow_array()) {
            $found = TRUE;
          } # while
          if($found == FALSE) {
            print OUTPUT_FILE "$probe2\t$mlg\t$cM\tIAState\tIAState\n";
          } # if
        } # if
      } # if
    } # for

    close OUTPUT_FILE;

    # print closing information
    message("Number of Confirmed:  $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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