package MenuMain;

=head1 NAME

MenuMain -- A Main Menu to run extropy

=head1 SYNOPSIS

MenuMain -> run;

=head1 DESCRIPTION

This package creates the Main Menu for extropy.  The
user interacts with Main Menu in order to run
the extropy system.

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::ConRead Extropy::CountCloneAnchors Extropy::CountContigAnchors Extropy::CrosscheckLocusNames Extropy::DBManager Extropy::EndMatchesRead Extropy::EstRead Extropy::FpcRead Extropy::Gff Extropy::Help Extropy::LocusRead Extropy::Menu Extropy::MenuGff Extropy::MenuProject Extropy::MtpRead Extropy::MlgRead Extropy::Project Extropy::ProjectCreate Extropy::ProjectPick Extropy::QtlRead Extropy::RelRead Extropy::SeqRead Extropy::Status Extropy::UpdateCloneAnchors Extropy::UpdateContigAnchors Extropy::UpdateLocusNames

=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::ConRead;
use Extropy::CountCloneAnchors;
use Extropy::CountContigAnchors;
use Extropy::CrosscheckLocusNames;
use Extropy::DBManager;
use Extropy::EndMatchesRead;
use Extropy::EstRead;
use Extropy::FpcRead;
use Extropy::Gff;
use Extropy::Help;
use Extropy::LocusRead;
use Extropy::Menu;
use Extropy::MenuGff;
use Extropy::MenuProject;
use Extropy::MtpRead;
use Extropy::MlgRead;
use Extropy::Project;
use Extropy::ProjectCreate;
use Extropy::ProjectPick;
use Extropy::QtlRead;
use Extropy::RelRead;
use Extropy::SeqRead;
use Extropy::Status;
use Extropy::UpdateCloneAnchors;
use Extropy::UpdateContigAnchors;
use Extropy::UpdateLocusNames;

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

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

=head2 run

  MenuMain->run;

Run the Main Menu.  The entire extropy system runs from the
Main Menu created by this method.

=cut

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

sub run {
  my $everything_ok = TRUE;

  # scroll the screen up for a clear work area
  my $lines_to_clear = 100;
  for(my $lcv = 0; $lcv < $lines_to_clear; $lcv++) {
    print "\n";
  } # for
  system "clear";

  # instantiate the DBManager object
  $db_manager = DBManager->new();

  # instantiate the Project object
  if($everything_ok) {
    if(!($project = Project->new)) {
      $everything_ok = FALSE;
    } # if
  } # if

  # instantiate the Configuration object
  if($everything_ok) {
    if(!($configuration = Configuration->new)) {
      $everything_ok = FALSE;
    } # if
  } # if

  # instantiate the Gff object
  if($everything_ok) {
    if(!($gff = Gff->new)) {
      $everything_ok = FALSE;
    } # if
  } # if

  $command = QUIT if(!$everything_ok);

  # get Main Menu input
  while($command != QUIT) {
    &print_main; 
    if($command == MENU_PROJECT) {
      MenuProject->run($configuration, $db_manager, $project);
    } # if
    elsif($command == MLG_READ) {
      MlgRead->new($configuration, $db_manager, $project);
    } # elsif
    elsif($command == LOCUS_READ) {
      LocusRead->new($configuration, $db_manager, $project);
    } # elsif
    elsif($command == FPC_READ) {
      FpcRead->new($configuration, $db_manager, $project);
    } # elsif
    elsif($command == QTL_READ) {
      QtlRead->new($configuration, $db_manager, $project);
    } # elsif
    elsif($command == END_MATCHES_READ) {
      EndMatchesRead->new($configuration, $db_manager, $project);
    } # elsif
    elsif($command == MTP_READ) {
      MtpRead->new($configuration, $db_manager, $project);
    } # elsif
    elsif($command == EST_READ) {
      EstRead->new($configuration, $db_manager, $project);
    } # elsif
    elsif($command == SEQ_READ) {
      SeqRead->new($configuration, $db_manager, $project);
    } # elsif
    elsif($command == REL_READ) {
      RelRead->new($configuration, $db_manager, $project);
    } # elsif
    elsif($command == CON_READ) {
      ConRead->new($configuration, $db_manager, $project);
    } # elsif
    elsif($command == CROSSCHECK_LOCUS_NAMES) {
      CrosscheckLocusNames->new($configuration, $db_manager, $project);
    } # elsif
    elsif($command == UPDATE_LOCUS_NAMES) {
      UpdateLocusNames->new($configuration, $db_manager, $project);
    } # elsif
    elsif($command == COUNT_CLONE_ANCHORS) {
      CountCloneAnchors->new($configuration, $db_manager, $project);
    } # elsif
    elsif($command == UPDATE_CLONE_ANCHORS) {
      UpdateCloneAnchors->new($configuration, $db_manager, $project);
    } # elsif
    elsif($command == COUNT_CONTIG_ANCHORS) {
      CountContigAnchors->new($configuration, $db_manager, $project);
    } # elsif
    elsif($command == UPDATE_CONTIG_ANCHORS) {
      UpdateContigAnchors->new($configuration, $db_manager, $project);
    } # elsif
    elsif($command == GFF_FILE_MENU) {
      MenuGff->run($configuration, $db_manager, $project, $gff);
    } # elsif
    elsif($command == STATUS) {
      Status->run($configuration, $db_manager, $project);
    } # elsif
    elsif($command == RESET) {
      message_start;
      if($project->{current_project} eq "") {
        message("A project must be active before it can be reset.");
      } # if
      else {
        message("You will have to start all over.");
        if(yes("Are you sure you want to reset the project?")) {
          $project->reset;
          message("Project reset.");
          $configuration->save($project);
        } # if
        else {
          message("Project not reset.");
        } # else
      } # else
      press_enter;
    } # elsif
    elsif($command == HELP) {
      Help->display($help_message_number);
    } # elsif
  } # while
  if($project->{current_project} ne "") {
    message_start;
    $configuration->save($project);
    print "\n";
  } # if
} # run

=head2 print_main()

  print_main();

Display the Main Menu.

=cut


# *******************************  print_main()  **********************

sub print_main() {
  my $menu_project_str = "";
  my $mlg_read_str = "";
  my $locus_read_str = "";
  my $fpc_read_str = "";
  my $qtl_read_str = "";
  my $end_matches_read_str = "";
  my $mtp_read_str = "";
  my $est_read_str = "";
  my $seq_read_str = "";
  my $rel_read_str = "";
  my $con_read_str = "";
  my $crosscheck_locus_names_str = "";
  my $update_locus_names_str = "";
  my $count_clone_anchors_str = "";
  my $update_clone_anchors_str = "";
  my $count_contig_anchors_str = "";
  my $update_contig_anchors_str = "";
  my $create_gff_file_str = "";
  my $reset_str = "";
  if($project->{current_project} eq "") {
    $menu_project_str = "(A)ctivate a project";
    $mlg_read_str = "- Read (M)LG File";
    $locus_read_str = "- Read (L)ocus File";
    $fpc_read_str = "- Read (F)PC File";
    $qtl_read_str = "- Read Q(T)L File";
    $end_matches_read_str = "- Read (E)nd Matches File";
    $mtp_read_str = "- Read MT(P) File";
    $est_read_str = "- Read EST File";
    $seq_read_str = "- Read Sequence File";
    $rel_read_str = "- Read Related Genes File";
    $con_read_str = "- Read Confirmed File";
    $crosscheck_locus_names_str = "- (C)rosscheck Locus Names";
    $update_locus_names_str = "- (U)pdate Locus Names";
    $count_clone_anchors_str ="- C(o)unt Clone Anchors";
    $update_clone_anchors_str = "- Up(d)ate Clone Anchors";
    $count_contig_anchors_str ="- Cou(n)t Contig Anchors";
    $update_contig_anchors_str = "- Update Cont(i)g Anchors";
    $create_gff_file_str = "- (G)FF File Menu";
    $reset_str = "- (R)eset Project";
  } # if
  else {
    $menu_project_str = "+ (A)ctivate a project";
    if($project->{mlg_file} eq "") {
      $mlg_read_str = "Read (M)LG File";
    } # if
    else {
      $mlg_read_str = "+ Read (M)LG File";
    } # else
    if($project->{locus_file} eq "") {
      $locus_read_str = "Read (L)ocus File";
    } # if
    else {
      $locus_read_str = "+ Read (L)ocus File";
    } # else
    if($project->{mlg_file} eq "") {
      $fpc_read_str = "- Read (F)PC File";
    } # if
    else {
      if($project->{fpc_file} eq "") {
        $fpc_read_str = "Read (F)PC File";
      } # if
      else {
        $fpc_read_str = "+ Read (F)PC File";
      } # else
    } # else
    if($project->{qtl_file} eq "") {
      $qtl_read_str = "Read Q(T)L File";
    } # if
    else {
      $qtl_read_str = "+ Read Q(T)L File";
    } # else
    if($project->{end_matches_file} eq "") {
      $end_matches_read_str = "Read (E)nd Matches File";
    } # if
    else {
      $end_matches_read_str = "+ Read (E)nd Matches File";
    } # else
    if($project->{mtp_file} eq "") {
      $mtp_read_str = "Read MT(P) File";
    } # if
    else {
      $mtp_read_str = "+ Read MT(P) File";
    } # else
    if($project->{est_file} eq "") {
      $est_read_str = "Read EST File";
    } # if
    else {
      $est_read_str = "+ Read EST File";
    } # else
    if($project->{seq_file} eq "") {
      $seq_read_str = "Read Sequence File";
    } # if
    else {
      $seq_read_str = "+ Read Sequence File";
    } # else
    if($project->{rel_file} eq "") {
      $rel_read_str = "Read Related Genes File";
    } # if
    else {
      $rel_read_str = "+ Read Related Genes File";
    } # else
    if($project->{con_file} eq "") {
      $con_read_str = "Read Confirmed File";
    } # if
    else {
      $con_read_str = "+ Read Confirmed File";
    } # else
    if($project->{locus_names_crosschecked} == TRUE) {
      $crosscheck_locus_names_str = "+ (C)rosscheck Locus Names";
    } # if
    else {
      if(($project->{locus_file} ne "") &&
        ($project->{fpc_file} ne "")) {
          $crosscheck_locus_names_str = "(C)rosscheck Locus Names";
      } # if
      else {
        $crosscheck_locus_names_str = "- (C)rosscheck Locus Names";
      } # else
    } # else
    if($project->{locus_names_updated} == TRUE) {
      $update_locus_names_str = "+ (U)pdate Locus Names";
    } # if
    else {
      if($project->{locus_names_crosschecked} == TRUE) {
        $update_locus_names_str = "(U)pdate Locus Names";
      } # if
      else {
        $update_locus_names_str = "- (U)pdate Locus Names";
      } # else
    } # else
    if($project->{clone_anchors_counted} == TRUE) {
      $count_clone_anchors_str = "+ C(o)unt Clone Anchors";
    } # if
    else {
      if($project->{locus_names_updated} == TRUE) {
        $count_clone_anchors_str = "C(o)unt Clone Anchors";
      } # if
      else {
        $count_clone_anchors_str = "- C(o)unt Clone Anchors";
      } # else
    } # else
    if($project->{clone_anchors_updated} == TRUE) {
      $update_clone_anchors_str = "+ Up(d)ate Clone Anchors";
    } # if
    else {
      if($project->{clone_anchors_counted} == TRUE) {
        $update_clone_anchors_str = "Up(d)ate Clone Anchors";
      } # if
      else {
        $update_clone_anchors_str = "- Up(d)ate Clone Anchors";
      } # else
    } # else
    if($project->{contig_anchors_counted} == TRUE) {
      $count_contig_anchors_str = "+ Cou(n)t Contig Anchors";
    } # if
    else {
      if($project->{clone_anchors_counted} == TRUE) {
        $count_contig_anchors_str = "Cou(n)t Contig Anchors";
      } # if
      else {
        $count_contig_anchors_str = "- Cou(n)t Contig Anchors";
      } # else
    } # else
    if($project->{contig_anchors_updated} == TRUE) {
      $update_contig_anchors_str = "+ Update Cont(i)g Anchors";
    } # if
    else {
      if($project->{contig_anchors_counted} == TRUE) {
        $update_contig_anchors_str = "Update Cont(i)g Anchors";
      } # if
      else {
        $update_contig_anchors_str = "- Update Cont(i)g Anchors";
      } # else
    } # else
    if($project->{gff_file_created} == TRUE) {
      $create_gff_file_str = "+ (G)FF File Menu";
    } # if
    else {
      if($project->{contig_anchors_updated}== TRUE) {
        $create_gff_file_str = "(G)FF File Menu";
      } # if
      else {
        $create_gff_file_str = "- (G)FF File Menu";
      } # else
    } # else
    $reset_str = "(R)eset Project";
  } # else
  $command = Menu->menu($menu_project_str, MENU_PROJECT,
                        $mlg_read_str, MLG_READ,
                        $locus_read_str, LOCUS_READ,
                        $fpc_read_str, FPC_READ,
                        $qtl_read_str, QTL_READ,
                        $end_matches_read_str, END_MATCHES_READ,
                        $mtp_read_str, MTP_READ,
                        $est_read_str, EST_READ,
                        $seq_read_str, SEQ_READ,
                        $rel_read_str, REL_READ,
                        $con_read_str, CON_READ,
                        $crosscheck_locus_names_str, CROSSCHECK_LOCUS_NAMES,
                        $update_locus_names_str, UPDATE_LOCUS_NAMES,
                        $count_clone_anchors_str, COUNT_CLONE_ANCHORS,
                        $update_clone_anchors_str, UPDATE_CLONE_ANCHORS,
                        $count_contig_anchors_str, COUNT_CONTIG_ANCHORS,
                        $update_contig_anchors_str, UPDATE_CONTIG_ANCHORS,
                        $create_gff_file_str, GFF_FILE_MENU,
                        "(S)tatus", STATUS,
                        $reset_str, RESET,
                        "(H)elp", HELP,
                        "(Q)uit", QUIT);
  $help_message_number = 1 if($command == HELP);
} # print_main

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