package PGF::GapResolution::ParseScaffInfo;

=head1 NAME

PGF::GapResolution::ParseScaffInfo

=head1 SYNOPSIS

use PGF::GapResolution::ParseScaffInfo;
my $obj = PGF::GapResolution::ParseScaffInfo->new($scaffInfoFile);
my $gapName = $obj->getGapName();
my $gapSize = $obj->getGapSize();
my $leftContig = $obj->getLeftContig();
my $leftContigLength = $obj->getLeftContigLength();
my $rightContig = $obj->getRightContig();
my $rightContigLength = $obj->getRightContigLength();
my $scaffoldName = $obj->getScaffoldName();

=head1 DESCRIPTION

This module parses the scaffinfo.txt file generated by createSubProject.pl
as part of the Gap Resolution sub system and contains access methods to the
data.

The format of the $scaffInfoFile mentioned above are as follows, separated by
a tab:

  1. <gap name>
  2. <gap size>
  3. <left contig length>
  4. <left contig>
  5. <right contig length>
  6. <right contig>
  7. <scaffold name>

=head1 AUTHOR(s)

Stephan Trong

=head1 HISTORY

=over

=item *

Stephan Trong 12/09/2008 Creation

=back

=cut

#============================================================================#
use strict;
use Carp;
use Carp qw(cluck);
use FindBin qw($RealBin);
use lib "$FindBin::RealBin/../lib";
use PGF::Utilities::Properties;

my $_DEBUG = 0;
my $_configFile = defined $ENV{GAPRES_CONFIG} ?
    $ENV{GAPRES_CONFIG} : "$RealBin/../config/gapRes.config";
my $_OBJ_PROPS = PGF::Utilities::Properties->new(-configFile=>$_configFile);
   $_OBJ_PROPS->setExceptionIfEntryNotFound(1); # confess if entry in config file
                                               # is not found.
#============================================================================#
sub new {
    
    my $class = shift;
    my $scaffInfoFile = shift;
    
    if ( !-s $scaffInfoFile ) {
        confess "ERROR: file $scaffInfoFile does not exists or is zero size.\n";
    }
    
    
    my @fileEntries = _parseFile($scaffInfoFile);
    my $self = { _entries=>\@fileEntries };
    bless $self, $class;
    
    return $self;

}

#============================================================================#
sub _parseFile {
    
    my $file = shift;
    
    unless (open FH, $file ) {
        confess "ERROR: failed to open file $file: $!";
    }
    chomp( my $entry = <FH> );
    close FH;
    
    my @entries = split /\t/, $entry;
    
    if ( @entries < 7 ) {
        confess "ERROR: $file does not contain a vaild entry.\n";
    }
    
    return @entries;
    
}

#============================================================================#
sub getGapName {
    
    my $self = shift;
    return $self->{_entries}[0];
}

#============================================================================#
sub getGapSize {
    
    my $self = shift;
    return $self->{_entries}[1];
}

#============================================================================#
sub getLeftContigLength {
    
    my $self = shift;
    return $self->{_entries}[2];
}

#============================================================================#
sub getLeftContig {
    
    my $self = shift;
    return $self->{_entries}[3];
}

#============================================================================#
sub getRightContigLength {
    
    my $self = shift;
    return $self->{_entries}[4];
}

#============================================================================#
sub getRightContig {
    
    my $self = shift;
    return $self->{_entries}[5];
}

#============================================================================#
sub getScaffoldName {
    
    my $self = shift;
    return $self->{_entries}[6];
}

#============================================================================#
1;