package SpectraDescriptionSetParametersParser;
use strict;
use Carp;

use 5.008;
use strict;
use warnings;

require Exporter;

our @ISA = qw(Exporter);

# Items to export into callers namespace by default. Note: do not export
# names by default without a very good reason. Use EXPORT_OK instead.
# Do not simply export all your public functions/methods/constants.

# This allows declaration	use SpectraDescriptionSetParametersParser ':all';
# If you do not need this, moving things directly into @EXPORT or @EXPORT_OK
# will save memory.
our %EXPORT_TAGS = ( 'all' => [ qw(
	
) ] );

our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } );

our @EXPORT = qw(
	
);

our $VERSION = '5.8';



# Preloaded methods go here.

sub new 
{
    my $class = shift;
    my %args = @_;
    my $self = {};
    $self->{mzXML_file} = undef;
    $self->{mzXML_schema} = undef;
    $self->{conversion_software_name} = undef;
    $self->{conversion_software_version} = undef;
    $self->{instrument_model_name} = undef;
    bless ($self, $class);
    return $self;
}


sub setMzXML_file
{
    my ($self, $file) = @_;
    croak("missing argument to setMzXML_file") unless defined $file;
    $self->{mzXML_file} = $file;
}

sub getMzXML_schema 
{
    my ($self) = @_;
    return $self->{mzXML_schema};
}


sub getConversion_software_name
{
    my ($self) = @_;
    return $self->{conversion_software_name};
}


sub getConversion_software_version
{
    my ($self) = @_;
    return $self->{conversion_software_version};
}


sub getInstrument_model_name
{
    my ($self) = @_;
    return $self->{instrument_model_name};
}


sub parse
{
    my ($self) = @_;
    croak("missing mzXML_file, please use setMzXML_file(xx)") 
        unless defined $self->{mzXML_file};

    my $infile = $self->{mzXML_file};


    my ($schema, $model_name, $software_name,
    $software_version);

    open(INFILE, "<$infile") or die "cannot open $infile for reading ($!)";

    while (my $line = <INFILE>)
    {
        chomp($line);

        ## recent schema:
        if ($line =~ /.+schemaLocation=\".+\/(.+)\/schema_revision\/(.+)\/(.+\.xsd)\">/)
        {
            $schema = $2;
        }

        ## former MsXML schema:
        ## xsi:schemaLocation="http://sashimi.sourceforge.net/schema/ http://sashimi.sourceforge.net/schema/MsXML.xsd
        if ($line =~ /.+schemaLocation=\".+\/(.+)\/schema\/(.+)\.xsd\"/ )
        {
            $schema = $2;
        }

        if ($line =~ /\<msManufacturer\scategory=\".+\"\svalue=\"(.+)\"\/\>/)
        {
            $model_name = $1;
        }
        if ($line =~ /\<msModel\scategory=\".+\"\svalue=\"(.+)\"\/\>/)
        {
            $model_name = $model_name . " $1";
        }

        ## former MsXML schema:
        if ($line =~ /\<instrument\smanufacturer=\"(.+)\"/ )
        {
            $model_name = $1;

            ## read the next line, and get model name
            $line = <INFILE>;
            chomp($line);
            $line =~ /\<instrument\smanufacturer=\"(.+)\"/;

            $model_name = $model_name . " $1";

        }

        if ($line =~ /\<software\stype=\"conversion(.+)/)
        {

	    #### why oh why aren't we using an xml parser?
	    my $morecontent = $1;
	    if ($morecontent =~ /name\s*=\s*\"(.*?)\"/) {
	      $software_name = $1;
	    }
	    if ($morecontent =~ /version\s*=\s*\"(.*?)\"/) {
	      $software_version = $1;
	    }


            $line = <INFILE>;

            chomp($line);

            if ($line =~ /.+name=\"(.+)\"/)
            {
                $software_name = $1;
            } else
            {
                carp "[WARN] please edit parser to pick up software attributes";
            }

            $line = <INFILE>;

            chomp($line);

            if ($line =~ /.+version=\"(.+)\"/)
            {
                $software_version = $1;
            }

            last; ## done
        }

    }

    close(INFILE) or die "Cannot close $infile";

    if ($software_version eq "")
    {
        carp "[WARN] please edit parser to pick up conversion_software_version for $infile";
    } 

    $self->{conversion_software_version} = $software_version;

    if ($software_name eq "")
    {
        carp "[WARN] please edit parser to pick up conversion_software_name for $infile";
    }

    $self->{conversion_software_name} = $software_name;

    if ($schema eq "")
    {
        carp "[WARN] please edit parser to pick up $schema for $infile";
    } 

    $self->{mzXML_schema} = $schema;

    if ($model_name eq "")
    {
        carp "[WARN] please edit parser to pick up instrument_model_name for $infile";
    } 

    $self->{instrument_model_name} = $model_name;

}



1;
__END__
# Below is stub documentation for your module. You'd better edit it!

=head1 SpectraDescriptionSetParametersParser


=head1 SYNOPSIS

SpectraDescriptionSetParametersParser does a quick parse
of an mzXML file to get the handful of information needed for
database attributes in PeptideAtlas table spectra_description_set,
and needed for versioning, etc.

USAGE:

use SpectraDescriptionSetParametersParser;

my $spectrum_parser = new SpectraDescriptionSetParametersParser();

$spectrum_parser->setMzXML_file("/path/to/file.mzXML");

$spectrum_parser->parse();

my $mzXML_schema = $spectrum_parser->getMzXML_schema();

my $conversion_software_name = getConversion_software_name();

my $conversion_software_version = getConversion_software_version();



=head1 ABSTRACT

   see above


=head1 DESCRIPTION

  see above

=head2 EXPORT

None by default.



=head1 SEE ALSO


=head1 AUTHOR Nichole King

=head1 COPYRIGHT AND LICENSE


This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself. 

=cut