package EstRead;

=head1 NAME

LocusRead -- Read an EST file and save the pertinent information into the
database

=head1 SYNOPSIS

my $boolean = EstRead -> new;

=head1 DESCRIPTION

This package reads an EST file and saves the
pertinent data into the database.  EstRead, 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 = EstRead->new;

Reads an EST 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->{est_file} ne "") {
      message("Data from EST file $project->{est_file}");
      message("is already in the database.");
      if(yes("Refresh the database from this file?")) {
        $file_name = $project->{est_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;
        $file_name = prompt("Enter path and EST file name");
      } # if
      if($file_name eq "Q") {
        $loop = FALSE;
        $file_obtained = FALSE;
      } # if
      elsif(file_name_ok($file_name, $configuration, $db_manager, $project)) {
        $loop = FALSE;
        $file_obtained = TRUE;
      } # elsif
      else {
        $file_obtained = FALSE;
        if(!yes("Try another file name?")) {
          $loop = FALSE;
        } # if
      } # else
    } # while
  } # else

  if($file_obtained) {
    # save the configuration
    $project->{est_file} = $file_name;
    $configuration->save($project);
    press_enter;
    TRUE;
  } # if
  else {
    press_enter;
    FALSE;
  } # else
} # new
# ********************************  file_name_ok  ******************************

=head2 project_name_ok

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

Determines if a file name is acceptable.  If the file name is ok, then the EST 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 $project = 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 EST input file
    message("EST file $file_name opened");
    message("Connecting to the database.");
    $db_manager->connect;
    message("Deleting any previous est data in the database.");
    $db_manager->execute("delete from est");
    message("Entering data into the database...");

    # read the input file
    my @file_array = <INPUT_FILE>;
    close INPUT_FILE;
    $number_lines = scalar(@file_array);

    my $clone = "";
    my $est = "";
    my $comment = "";

    # look at each line in the input file
    for(my $line_number=0; $line_number < $number_lines; $line_number++) {
      my $current_line = $file_array[$line_number];
      chomp $current_line;
      my @field_array = split /\t/, $current_line;
      $clone = $field_array[0];
      $est = $field_array[1];
      if($field_array[2]) {
        $comment = $field_array[2];
        # trim the white space
        $comment =~ s/^\s*//;
        $comment =~ s/\s*$//;
      } #
      else {
        $comment = "";
      } # else
      $comment = "" if ($comment eq "EST");
      $comment = substr($comment, 1) if(substr($comment, 0, 1) eq "\"");
      $comment = substr($comment, 0,-1) if(substr($comment, -1, 1) eq "\"");
      # trim the white space (again)
      $comment =~ s/^\s*//;
      $comment =~ s/\s*$//;
      $comment = substr($comment, 0,-1) if(substr($comment, -1, 1) eq ".");
      $comment = substr($comment, 0,-1) if(substr($comment, -1, 1) eq ",");

      # Save the relations in the clone2locus database table
      my $eid = $db_manager->{dbh}->quote("");
      my $db_clone = $db_manager->{dbh}->quote("$clone");
      my $db_est = $db_manager->{dbh}->quote("$est");
      my $db_comment = $db_manager->{dbh}->quote("$comment");
      $db_manager->execute("insert into est values($eid, $db_clone, $db_est, $db_comment)");

} # for

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

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

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

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