package MenuGff;

=head1 NAME

MenuGff -- A menu to create a GFF file

=head1 SYNOPSIS

MenuGff -> run;

=head1 DESCRIPTION

This package creates a GFF Menu for extropy.  The
user interacts with GFF Menu in order to create a
GFF file.

The only method is run.

=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::Configuration Extropy::DBManager Extropy::Project Extropy::ProjectCreate Extropy::ProjectPick 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;
use Extropy::Configuration;
use Extropy::DBManager;
# use Extropy::Help;
# use Extropy::Menu;
use Extropy::Project;
use Extropy::ProjectCreate;
use Extropy::ProjectPick;

# package variables
my $configuration;
my $db_manager;
my $project;
my $gff;
my $command = NONE;
my $help_message_number = 0;

# ********************************  run  ******************************

=head2 run

  MenuProject->run;

Run the Project Menu, which allows the user to select an existing
project or start a new one.

=cut

# ---------------------------------------------------------------------

sub run {
  my $self = shift;
  $configuration = shift;
  $db_manager = shift;
  $project = shift;
  $gff = shift;

  my $proceed = TRUE;
  while($proceed) {
    &print_menu; 
    if($command == HELP) {
      Help->display($help_message_number);
    } # if
    elsif($command == QUIT) {
      $proceed = FALSE;
    } # elsif
    elsif($command == GFF_LOCI) {
      message_start;
      if($project->{locus_names_updated}) {
        if($gff->{loci} == TRUE) {
          $gff->{loci} = FALSE;
          message("The loci will NOT be included in the GFF file");
        } # if
        else {
          $gff->{loci} = TRUE;
          message("The loci will be included in the GFF file");
        } # else
      } # if
      else {
        message("The loci names must be updated, first");
      } # else
      press_enter;
    } # elsif
    elsif($command == GFF_CLONES) {
      message_start;
      if($project->{clone_anchors_updated}) {
        if($gff->{clones} == TRUE) {
          $gff->{clones} = FALSE;
          message("The clones will NOT be included in the GFF file");
        } # if
        else {
          $gff->{clones} = TRUE;
          message("The clones will be included in the GFF file");
        } # else
      } # if
      else {
        message("The clone anchors must be updated, first");
      } # else
      press_enter;
    } # elsif
    elsif($command == GFF_CONTIGS) {
      message_start;
      if($project->{contig_anchors_updated}) {
        if($gff->{contigs} == TRUE) {
          $gff->{contigs} = FALSE;
          message("The contigs will NOT be included in the GFF file");
        } # if
        else {
          $gff->{contigs} = TRUE;
          message("The contigs will be included in the GFF file");
        } # else
      } # if
      else {
        message("The contig anchors must be updated, first");
      } # else
      press_enter;
    } # elsif
    elsif($command == GFF_QTLS) {
      message_start;
      if($project->{qtl_file} ne "") {
        if($gff->{qtls} == TRUE) {
          $gff->{qtls} = FALSE;
          message("The QTL's will NOT be included in the GFF file");
        } # if
        else {
          $gff->{qtls} = TRUE;
          message("The QTL's will be included in the GFF file");
        } # else
      } # if
      else {
        message("The QTL's must be read, first");
      } # else
      press_enter;
    } # elsif
    elsif($command == GFF_ENDS) {
      message_start;
      if($project->{end_matches_file} ne "") {
        if($gff->{ends} == TRUE) {
          $gff->{ends} = FALSE;
          message("The end matches will NOT be included in the GFF file");
        } # if
        else {
          $gff->{ends} = TRUE;
          message("The end matches will be included in the GFF file");
        } # else
      } # if
      else {
        message("The end matches must be read, first");
      } # else
      press_enter;
    } # elsif
    elsif($command == GFF_MTPS) {
      message_start;
      if($project->{mtp_file} ne "") {
        if($gff->{mtps} == TRUE) {
          $gff->{mtps} = FALSE;
          message("The MTP's will NOT be included in the GFF file");
        } # if
        else {
          $gff->{mtps} = TRUE;
          message("The MTP's will be included in the GFF file");
        } # else
      } # if
      else {
        message("The MTP's must be read, first");
      } # else
      press_enter;
    } # elsif

    elsif($command == GFF_ESTS) {
      message_start;
      if($project->{est_file} ne "") {
        if($gff->{ests} == TRUE) {
          $gff->{ests} = FALSE;
          message("The EST's will NOT be included in the GFF file");
        } # if
        else {
          $gff->{ests} = TRUE;
          message("The EST's will be included in the GFF file");
        } # else
      } # if
      else {
        message("The EST's must be read, first");
      } # else
      press_enter;
    } # elsif

    elsif($command == GFF_SEQ) {
      message_start;
      if($project->{seq_file} ne "") {
        if($gff->{seq} == TRUE) {
          $gff->{seq} = FALSE;
          message("The Sequences will NOT be included in the GFF file");
        } # if
        else {
          $gff->{seq} = TRUE;
          message("The Sequences will be included in the GFF file");
        } # else
      } # if
      else {
        message("The Sequences must be read, first");
      } # else
      press_enter;
    } # elsif

    elsif($command == GFF_REL) {
      message_start;
      if($project->{rel_file} ne "") {
        if($gff->{rel} == TRUE) {
          $gff->{rel} = FALSE;
          message("The Related Genes will NOT be included in the GFF file");
        } # if
        else {
          $gff->{rel} = TRUE;
          message("The Related Genes will be included in the GFF file");
        } # else
      } # if
      else {
        message("The Related Genes must be read, first");
      } # else
      press_enter;
    } # elsif

    elsif($command == GFF_CON) {
      message_start;
      if($project->{con_file} ne "") {
        if($gff->{con} == TRUE) {
          $gff->{con} = FALSE;
          message("The Confirmed will NOT be included in the GFF file");
        } # if
        else {
          $gff->{con} = TRUE;
          message("The Confirmed will be included in the GFF file");
        } # else
      } # if
      else {
        message("The Confirmed must be read, first");
      } # else
      press_enter;
    } # elsif

    elsif($command == GFF_ALL) {
      message_start;

      if(!$project->{locus_names_updated}) {
        message("The loci names must be updated, first");
      } # if
      else {
        $gff->{loci} = TRUE;
        message("The loci will be included in the GFF file");
      } # else

      if(!$project->{clone_anchors_updated}) {
        message("The clone anchors must be updated, first");
      } # if
      else {
        $gff->{clones} = TRUE;
        message("The clones will be included in the GFF file");
      } # else

      if(!$project->{contig_anchors_updated}) {
        message("The contig anchors must be updated, first");
      } # if
      else {
        $gff->{contigs} = TRUE;
        message("The contigs will be included in the GFF file");
      } # else

      if($project->{qtl_file} eq "") {
        message("The QTL's must be read, first");
      } # if
      else {
        $gff->{qtls} = TRUE;
        message("The QTL's will be included in the GFF file");
      } # else

      if($project->{end_matches_file} eq "") {
        message("The end matches must be read, first");
      } # if
      else {
        $gff->{ends} = TRUE;
        message("The end matches will be included in the GFF file");
      } # else

      if($project->{mtp_file} eq "") {
        message("The MTP's must be read, first");
      } # if
      else {
        $gff->{mtps} = TRUE;
        message("The MTP's will be included in the GFF file");
      } # else

      if($project->{est_file} eq "") {
        message("The EST's must be read, first");
      } # if
      else {
        $gff->{ests} = TRUE;
        message("The EST's will be included in the GFF file");
      } # else

      if($project->{seq_file} eq "") {
        message("The Sequences must be read, first");
      } # if
      else {
        $gff->{seq} = TRUE;
        message("The Sequences will be included in the GFF file");
      } # else

      if($project->{rel_file} eq "") {
        message("The Related Genes must be read, first");
      } # if
      else {
        $gff->{rel} = TRUE;
        message("The Related Genes will be included in the GFF file");
      } # else

      if($project->{con_file} eq "") {
        message("The Confirmed must be read, first");
      } # if
      else {
        $gff->{con} = TRUE;
        message("The Confirmed will be included in the GFF file");
      } # else

      press_enter;
    } # elsif
    elsif($command == GFF_WRITE) {
      $gff->write($db_manager, $project);
    } # elsif
  } # while

  $command = NONE if($command != QUIT);
  $command;
} # run

=head2 print_main()

  print_menu;

Display the menu.

=cut


# *******************************  print_menu  ************************

sub print_menu {
  my $loci_str = "Add (L)oci";
  if($gff->{loci} == TRUE) {
    $loci_str = "Remove (L)oci";
  } # if
  my $clones_str = "Add (C)lones";
  if($gff->{clones} == TRUE) {
    $clones_str = "Remove (C)lones";
  } # if
  my $contigs_str = "Add Conti(g)s";
  if($gff->{contigs} == TRUE) {
    $contigs_str = "Remove Conti(g)s";
  } # if
  my $qtls_str = "Add Q(T)L's";
  if($gff->{qtls} == TRUE) {
    $qtls_str = "Remove Q(T)L's";
  } # if
  my $ends_str = "Add (E)nd matches";
  if($gff->{ends} == TRUE) {
    $ends_str = "Remove (E)nd matches";
  } # if
  my $mtps_str = "Add MT(P)'s";
  if($gff->{mtps} == TRUE) {
    $mtps_str = "Remove MT(P)'s";
  } # if
  my $ests_str = "Add E(S)T's";
  if($gff->{ests} == TRUE) {
    $ests_str = "Remove E(S)T's";
  } # if
  my $seq_str = "Add Sequences";
  if($gff->{seq} == TRUE) {
    $seq_str = "Remove Sequences";
  } # if
  my $rel_str = "Add Related Genes";
  if($gff->{rel} == TRUE) {
    $rel_str = "Remove Related Genes";
  } # if
  my $con_str = "Add Confirmed";
  if($gff->{con} == TRUE) {
    $con_str = "Remove Confirmed";
  } # if
  $command = Menu->menu($loci_str, GFF_LOCI,
                        $clones_str, GFF_CLONES,
                        $contigs_str, GFF_CONTIGS,
                        $qtls_str, GFF_QTLS,
                        $ends_str, GFF_ENDS,
                        $mtps_str, GFF_MTPS,
                        $ests_str, GFF_ESTS,
                        $seq_str, GFF_SEQ,
                        $rel_str, GFF_REL,
                        $con_str, GFF_CON,
                        "Add (A)ll", GFF_ALL,
                        "Write GFF (F)ile", GFF_WRITE,
                        "(H)elp", HELP,
                        "(Q)uit", QUIT);
  $help_message_number = 101 if($command == HELP);
} # print_menu

1