package Project;

=head1 NAME

Project -- An object that keeps track of project information.

=head1 SYNOPSIS

my $project = Project->new;
my $boolean = Project->read;
my $boolean = Project->save;

Object hash entries:

  current_project           string
  mlg_file                  string
  locus_file                string
  fpc_file                  string
  qtl_file                  string
  end_matches_file          string
  mtp_file                  string
  est_file                  string
  seq_file                  string
  rel_file                  string
  con_file                  string
  locus_names_crosschecked  boolean
  locus_names_updated       boolean
  clone_anchors_counted     boolean
  clone_anchors_updated     boolean
  contig_anchors_counted    boolean
  contig_anchors_update     boolean
  gff_file_created          boolean
  ave_clone_length          bands
  band_factor               bases per band

=head1 DESCRIPTION

This object keeps track of the project information.

=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;

# package variables

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

=head2 new

  my $project = Project->new;

Creates an instance of the Project object.

=cut

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

sub new {
  # instantiate the oject
  my $self = {};
  bless $self;
  my $defined = TRUE;
  $self->{current_project} = "";
  $self->reset;

  # return values
  if($defined) {
    $self;
  } # if
  else {
    undef;
  } # else
} # new()

# ********************************  read  *****************************

=head2 read

  $project->read;

Reads the project configuration project_name.cfg file.

=cut

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

sub read {
  my $self = shift;
  my $error = FALSE;
  my $current_project = $self->{current_project};

  message("Reading the project configuration from $current_project.cfg");

  open(CFG_FILE, "<", "$current_project.cfg")
    or $error = TRUE;
  if($error) {
    message("Could not read $current_project.cfg");
    message("$!");
  } # if
  else {
    # The config file is open
    $self->reset;

    # read the configuration file
    my @file_array = <CFG_FILE>;
    for(my $lcv = 0; $lcv < scalar(@file_array); $lcv++) {
      my $current_line = $file_array[$lcv];
      next if($current_line =~ /^#/);
      chomp $current_line;
      next if($current_line =~ /^\s*$/);
      my @line_array = split /=/, $current_line;
      if($line_array[0] =~ /mlg_file/) {
        if($line_array[1]) {
          $self->{mlg_file} = $line_array[1];
        } # if
        else {
          $self->{mlg_file} = "";
        } # else
      } # if
      elsif($line_array[0] =~ /locus_file/) {
        if($line_array[1]) {
          $self->{locus_file} = $line_array[1];
        } # if
        else {
          $self->{locus_file} = "";
        } # else
      } # elsif
      elsif($line_array[0] =~ /fpc_file/) {
        if($line_array[1]) {
          $self->{fpc_file} = $line_array[1];
        } # if
        else {
          $self->{fpc_file} = "";
        } # else
      } # elsif
      elsif($line_array[0] =~ /qtl_file/) {
        if($line_array[1]) {
          $self->{qtl_file} = $line_array[1];
        } # if
        else {
          $self->{qtl_file} = "";
        } # else
      } # elsif
      elsif($line_array[0] =~ /end_matches_file/) {
        if($line_array[1]) {
          $self->{end_matches_file} = $line_array[1];
        } # if
        else {
          $self->{end_matches_file} = "";
        } # else
      } # elsif
      elsif($line_array[0] =~ /mtp_file/) {
        if($line_array[1]) {
          $self->{mtp_file} = $line_array[1];
        } # if
        else {
          $self->{mtp_file} = "";
        } # else
      } # elsif
      elsif($line_array[0] =~ /est_file/) {
        if($line_array[1]) {
          $self->{est_file} = $line_array[1];
        } # if
        else {
          $self->{est_file} = "";
        } # else
      } # elsif
      elsif($line_array[0] =~ /seq_file/) {
        if($line_array[1]) {
          $self->{seq_file} = $line_array[1];
        } # if
        else {
          $self->{seq_file} = "";
        } # else
      } # elsif
      elsif($line_array[0] =~ /rel_file/) {
        if($line_array[1]) {
          $self->{rel_file} = $line_array[1];
        } # if
        else {
          $self->{rel_file} = "";
        } # else
      } # elsif
      elsif($line_array[0] =~ /con_file/) {
        if($line_array[1]) {
          $self->{con_file} = $line_array[1];
        } # if
        else {
          $self->{con_file} = "";
        } # else
      } # elsif
      elsif($line_array[0] =~ /locus_names_crosschecked/) {
        if($line_array[1]) {
          $self->{locus_names_crosschecked} = $line_array[1];
        } # if
        else {
          $self->{locus_names_crosschecked} = FALSE;
        } # else
      } # elsif
      elsif($line_array[0] =~ /locus_names_updated/) {
        if($line_array[1]) {
          $self->{locus_names_updated} = $line_array[1];
        } # if
        else {
          $self->{locus_names_updated} = FALSE;
        } # else
      } # elsif
      elsif($line_array[0] =~ /clone_anchors_counted/) {
        if($line_array[1]) {
          $self->{clone_anchors_counted} = $line_array[1];
        } # if
        else {
          $self->{clone_anchors_counted} = FALSE;
        } # else
      } # elsif
      elsif($line_array[0] =~ /clone_anchors_updated/) {
        if($line_array[1]) {
          $self->{clone_anchors_updated} = $line_array[1];
        } # if
        else {
          $self->{clone_anchors_updated} = FALSE;
        } # else
      } # elsif
      elsif($line_array[0] =~ /contig_anchors_counted/) {
        if($line_array[1]) {
          $self->{contig_anchors_counted} = $line_array[1];
        } # if
        else {
          $self->{contig_anchors_counted} = FALSE;
        } # else
      } # elsif
      elsif($line_array[0] =~ /contig_anchors_updated/) {
        if($line_array[1]) {
          $self->{contig_anchors_updated} = $line_array[1];
        } # if
        else {
          $self->{contig_anchors_updated} = FALSE;
        } # else
      } # elsif
      elsif($line_array[0] =~ /gff_file_created/) {
        if($line_array[1]) {
          $self->{gff_file_created} = $line_array[1];
        } # if
        else {
          $self->{gff_file_created} = FALSE;
        } # else
      } # elsif
      elsif($line_array[0] =~ /ave_clone_length/) {
        if($line_array[1]) {
          $self->{ave_clone_length} = $line_array[1];
        } # if
        else {
          $self->{ave_clone_length} = -1;
        } # else
      } # elsif
      elsif($line_array[0] =~ /band_factor/) {
        if($line_array[1]) {
          $self->{band_factor} = $line_array[1];
        } # if
        else {
          $self->{band_factor} = -1;
        } # else
      } # elsif
    } # for

    message("The configuration was read");

  } # else
  close CFG_FILE;
} # read_project

# ********************************  reset *****************************

=head2 reset

  reset;

Resets the variables for the project.  For internal use, only.

=cut

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

sub reset {
  my $self = shift;

  $self->{mlg_file} = "";
  $self->{locus_file} = "";
  $self->{fpc_file} = "";
  $self->{qtl_file} = "";
  $self->{end_matches_file} = "";
  $self->{mtp_file} = "";
  $self->{est_file} = "";
  $self->{seq_file} = "";
  $self->{rel_file} = "";
  $self->{con_file} = "";
  $self->{locus_names_crosschecked} = FALSE;
  $self->{locus_names_updated} = FALSE;
  $self->{clone_anchors_counted} = FALSE;
  $self->{clone_anchors_updated} = FALSE;
  $self->{contig_anchors_counted} = FALSE;
  $self->{contig_anchors_updated} = FALSE;
  $self->{gff_file_created} = FALSE;
  $self->{ave_clone_length} = -1;
  $self->{band_factor} = -1;
} # reset

# ********************************  save  *****************************

=head2 save

  $project->save;

Saves the project configuration to the project_name.cfg file.

=cut

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

sub save {
  my $self = shift;
  my $error = FALSE;
  my $current_project = $self->{current_project};

  open(CFG_FILE, ">", "$current_project.cfg")
    or $error = TRUE;
  if($error) {
    message("Could not save to $current_project.cfg");
    message("$!");
  } # if
  else {
    print CFG_FILE "# $current_project.cfg\n";
    print CFG_FILE "# This is the project configuration file\n";
    print CFG_FILE "#   for the $current_project project for extropy.\n";
    print CFG_FILE "# This file is created automatically by extropy.\n";
    print CFG_FILE "# Any changes made directly to this file may be lost.\n";
    my $date = localtime;
    print CFG_FILE "# Last update:  $date\n\n";
    print CFG_FILE "mlg_file=$self->{mlg_file}\n";
    print CFG_FILE "locus_file=$self->{locus_file}\n";
    print CFG_FILE "fpc_file=$self->{fpc_file}\n";
    print CFG_FILE "qtl_file=$self->{qtl_file}\n";
    print CFG_FILE "end_matches_file=$self->{end_matches_file}\n";
    print CFG_FILE "mtp_file=$self->{mtp_file}\n";
    print CFG_FILE "est_file=$self->{est_file}\n";
    print CFG_FILE "seq_file=$self->{seq_file}\n";
    print CFG_FILE "rel_file=$self->{rel_file}\n";
    print CFG_FILE "con_file=$self->{con_file}\n";
    print CFG_FILE "locus_names_crosschecked=$self->{locus_names_crosschecked}\n";
    print CFG_FILE "locus_names_updated=$self->{locus_names_updated}\n";
    print CFG_FILE "clone_anchors_counted=$self->{clone_anchors_counted}\n";
    print CFG_FILE "clone_anchors_updated=$self->{clone_anchors_updated}\n";
    print CFG_FILE "contig_anchors_counted=$self->{contig_anchors_counted}\n";
    print CFG_FILE "contig_anchors_updated=$self->{contig_anchors_updated}\n";
    print CFG_FILE "gff_file_created=$self->{gff_file_created}\n";
    print CFG_FILE "ave_clone_length=$self->{ave_clone_length}\n";
    print CFG_FILE "band_factor=$self->{band_factor}\n";
    message("The project configuration was saved to $current_project.cfg");
  } # else
  close CFG_FILE;
} # save_project

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