package PGF::GapResolution::ParseGapValidationInfo;

=head1 NAME

PGF::GapResolution::ParseGapValidationInfo

=head1 SYNOPSIS

use PGF::GapResolution::ParseGapValidationInfo;

my $obj = PGF::GapResolution::ParseGapValidationInfo->new($validationInfoFile);
my $leftContig = $obj->getLeftContig();
my $rightContig = $obj->getRightContig();
my $leftContigLength = $obj->getLeftContigLength();
my $rightContigLength = $obj->getRightContigLength();
my ($leftStart,$leftEnd) = $obj->getLeftAnchorPos();
my ($rightStart,$rightEnd) = $obj->getRightAnchorPos();
my ($anchorStart,$anchorEnd) = $obj->getAnchorPos();
my $anchorDistance = $obj->getAnchorDistance();
my $gapSize = $obj->getGapSize();
my $gapSizeStdDev = $obj->getGapSizeStdDev();
my $numConsistentReadPairs = $obj->getNumConsistentReadPairs();
my $numInconsistentReadPairs = $obj->getNumInconsistentReadPairs();
my $pctConsistent = $obj->getPctConsistent();
my $avgConsensusQuality = $obj->getAvgConsensusQualityBetweenAnchors();
my $isDistanceValid = $obj->isDistanceValid();
my $isReadPairingValid = $obj->isReadPairingValid();
my $isQualityValid = $obj->isQualityValid();
my $status = $obj->isSuccessful();
my $designPrimer = $obj->doPrimerDesign();
my $comment = $obj->getComment();
    
=head1 DESCRIPTION

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

The format of the validinfo.txt are key/value pairs.  An example of

leftAnchorContig=name of contig
leftAnchorContigLength=number
leftAnchorStart=number
leftAnchorEnd=number
rightAnchorContig=name of contig
rightAnchorContigLength=number
rightAnchorStart=number
rightAnchorEnd=number
anchorStart=number
anchorEnd=number
anchorDistance=number
gapSize=number
gapSizeStdDev=number
numConsistentReadPairs=number
numInconsistentReadPairs=number
pctConsistent=number
avgConsensusQualityBetweenAnchors=number
isDistanceValid=0|1
isReadPairingValid=0|1
isQualityValid=0|1
status=PASS|FAIL
doPrimerDesign=0|1
comment=comment entry

=head1 AUTHOR(s)

Stephan Trong

=head1 HISTORY

=over

=item *

Stephan Trong 12/11/2008 Creation

=back

=cut

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

#============================================================================#
sub new {
    
    my $class = shift;
    my $file = shift;
    
    my %attribs = _parseFile($file);
    my $self = { _attribs=>\%attribs };
    bless $self, $class;
    
    return $self;

}

#============================================================================#
sub _parseFile {
    
    my $file = shift;
    
    my %attribs = ();
    
    unless (open FH, $file ) {
        confess "ERROR: failed to open file $file: $!";
    }
    
    while ( my $entry = <FH> ) {
        chomp $entry;
        next if !length $entry;
        if ( $entry =~ /^(.+)\s*=\s*(.+)$/ ) {
            $attribs{$1} = $2;
        }
    }
        
    close FH;
    
    return %attribs;
}

#============================================================================#
sub getLeftContig {
    return $_[0]->{_attribs}{leftAnchorContig} || '';
}

#============================================================================#
sub getRightContig {
    return $_[0]->{_attribs}{rightAnchorContig} || '';
}

#============================================================================#
sub getLeftContigLength{
    return $_[0]->{_attribs}{leftAnchorContigLength} || '';
}

#============================================================================#
sub getRightContigLength{
    return $_[0]->{_attribs}{rightAnchorContigLength} || '';
}

#============================================================================#
sub getLeftAnchorPos {
    return $_[0]->{_attribs}{leftAnchorStart},
           $_[0]->{_attribs}{leftAnchorEnd} || '';
}

#============================================================================#
sub getRightAnchorPos {
    return $_[0]->{_attribs}{rightAnchorStart},
           $_[0]->{_attribs}{rightAnchorEnd} || '';
}

#============================================================================#
sub getAnchorPos{
    return $_[0]->{_attribs}{anchorStart},
           $_[0]->{_attribs}{anchorEnd} || '';
}

#============================================================================#
sub getAnchorDistance {
    return $_[0]->{_attribs}{anchorDistance} || '';
}

#============================================================================#
sub getGapSize {
    return $_[0]->{_attribs}{gapSize} || '';
}

#============================================================================#
sub getGapSizeStdDev {
    return $_[0]->{_attribs}{gapSizeStdDev} || '';
}

#============================================================================#
sub getNumConsistentReadPairs {
    return $_[0]->{_attribs}{numConsistentReadPairs} || '';
}

#============================================================================#
sub getNumInconsistentReadPairs {
    return $_[0]->{_attribs}{numInconsistentReadPairs} || '';
}

#============================================================================#
sub getPctConsistent{
    return $_[0]->{_attribs}{pctConsistent} || '';
}

#============================================================================#
sub getAvgConsensusQualityBetweenAnchors{
    return $_[0]->{_attribs}{avgConsensusQualityBetweenAnchors} || '';
}

#============================================================================#
sub isDistanceValid {
    return $_[0]->{_attribs}{isDistanceValid} || '';
}

#============================================================================#
sub isReadPairingValid {
    return $_[0]->{_attribs}{isReadPairingValid} || '';
}

#============================================================================#
sub isQualityValid {
    return $_[0]->{_attribs}{isQualityValid} || '';
}

#============================================================================#
sub doPrimerDesign {
    return $_[0]->{_attribs}{doPrimerDesign} || '';
}

#============================================================================#
sub isSuccessful {
    if ( $_[0]->{_attribs}{status} eq 'SUCCESSFUL' ||
         $_[0]->{_attribs}{status} eq 'PASS' ) {
        # Status=SUCCESSFUL is deprecated but checked for backwards compatibility.
        return 1;
    } else {
        return 0;
    }
}

#============================================================================#
sub getComment {
    return $_[0]->{_attribs}{comment} || '';
}

#============================================================================#
sub getAllAttribs {
    return %{$_[0]->{_attribs}};
}

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