# BioPerl module for Bio::Factory::EMBOSS
# Please direct questions and support issues to <bioperl-l@bioperl.org>
# Cared for by Heikki Lehvaslaiho <heikki-at-bioperl-dot-org>
# Copyright Heikki Lehvaslaiho
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code

=head1 NAME

Bio::Factory::EMBOSS - EMBOSS application factory class


  # Get an EMBOSS factory
  use Bio::Factory::EMBOSS;
  $f = Bio::Factory::EMBOSS -> new();
  # Get an EMBOSS application  object from the factory
  $water = $f->program('water') || die "Program not found!\n";

  # Here is an example of running the application - water can
  # compare 1 sequence against 1 or more sequences using Smith-Waterman.
  # Pass a Sequence object and a reference to an array of objects.

  my $wateroutfile = 'out.water';
  $water->run({-asequence => $seq_object,
               -bsequence => \@seq_objects,
               -gapopen   => '10.0',
               -gapextend => '0.5',
               -outfile   => $wateroutfile});

  # Now you might want to get the alignment
  use Bio::AlignIO;
  my $alnin = Bio::AlignIO->new(-format => 'emboss',
                                -file   => $wateroutfile);

  while ( my $aln = $alnin->next_aln ) {
      # process the alignment -- these will be Bio::SimpleAlign objects


The EMBOSS factory class encapsulates access to EMBOSS programs.  A
factory object allows creation of only known applications.

If you want to check command line options before sending them to the
program set $prog-E<gt>verbose to positive integer. The value is
passed on to programs objects and the ADC description of the available
command line options is parsed and compared to input.

See also L<Bio::Tools::Run::EMBOSSApplication> and


=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to the
Bioperl mailing lists  Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Support

Please direct usage questions or support issues to the mailing list:


rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.  Bug reports can be submitted via the


=head1 AUTHOR - Heikki Lehvaslaiho

Email heikki-at-bioperl-dot-org


The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _


# Let the code begin...

package Bio::Factory::EMBOSS;
use vars qw(@ISA $EMBOSSVERSION);
use strict;

use Bio::Root::Root;
use Bio::Tools::Run::EMBOSSApplication;
use Bio::Factory::ApplicationFactoryI;
@ISA = qw(Bio::Root::Root Bio::Factory::ApplicationFactoryI );


sub new {
    my($class,@args) = @_;
    my $self = $class->SUPER::new(@args);
    # set up defaults

    my($location) = $self->_rearrange([qw(LOCATION )], @args);

    $self->{ '_programs' } = {};
    $self->{ '_programgroup' } = {};
    $self->{ '_groups' } = {};

    $self->location($location) if $location;

    $self->_program_list; # retrieve info about available programs

    return $self;

=head2 location

 Title   : location
 Usage   : $embossfactory->location
 Function: get/set the location of EMBOSS programs.
           Valid values are 'local' and 'novella'.
 Returns : string, defaults to 'local'
 Args    : string


sub location {
    my ($self, $value) = @_;
    my %location = ('local' => '1',
                    'novella' => '1'
    if (defined $value) {
        $value = lc $value;
        if ($location{$value}) {
            $self->{'_location'} = $value;
        } else {
            $self->warn("Value [$value] not a valid value for ".
                        "location(). Defaulting to [local]");
            $self->{'_location'} = 'local';
    $self->{'_location'} ||= 'local';
    return $self->{'_location'};

=head2 program

 Title   : program
 Usage   : $embossfactory->program('program_name')
 Function: Creates a representation of a single EMBOSS program and issues a
           warning if the program was not found.
 Returns : Bio::Tools::Run::EMBOSSApplication object or undef
 Args    : string, program name


sub program {
    my ($self, $value) = @_;

    unless( $self->{'_programs'}->{$value} ) {
        $self->warn("Application [$value] is not available!");
        return undef;
    my $attr = {};
    $attr->{name} = $value;
    $attr->{verbose} = $self->verbose;

    my $appl = Bio::Tools::Run::EMBOSSApplication->new($attr);
    return $appl;

=head2 version

 Title   : $self->version
 Usage   : $embossfactory->version()
 Function: gets the version of EMBOSS programs
 Throws  : if EMBOSS suite is not accessible
 Returns : version value
 Args    : None


sub version {
    my ($self) = @_;
    my $version = `embossversion -auto`;
    $self->throw("EMBOSS suite of programs is not available") if $?;
    chop $version;

    # compare versions
    $self->throw("EMBOSS has to be at least version $EMBOSSVERSION got $version\n")
        if $version lt $EMBOSSVERSION;

    return $version;

=head2 Programs

These methods allow the programmer to query the EMBOSS suite and find
out which program names can be used and what arguments can be used.

=head2 program_info

 Title   : program_info
 Usage   : $embossfactory->program_info('emma')
 Function: Finds out if the program is available.
 Returns : definition string of the program, undef if program name not known
 Args    : string, prgramname


sub program_info {
    my ($self, $value) = @_;
    return $self->{'_programs'}->{$value};

=head2 Internal methods

Do not call these methods directly

=head2 _program_list

 Title   : _program_list
 Usage   : $embossfactory->_program_list()
 Function: Finds out what programs are available.
           Writes the names into an internal hash.
 Returns : true if successful
 Args    : None


sub _program_list {
    my ($self) = @_;
    if( $^O =~ /Mac/i ) { return; }
        my $null = ($^O =~ m/mswin/i) ? 'NUL' : '/dev/null';
        local * SAVERR;
        open SAVERR, ">&STDERR";
        open STDERR, ">$null";
        open(WOSSOUT, "wossname -auto |") || return;
        open STDERR, ">&SAVERR";

    local $/ = "\n\n";
    while(<WOSSOUT> ) {
        my ($groupname) = (/^([A-Z][A-Z0-9 ]+)$/m);
        #print $groupname, "\n" if $groupname;
        $self->{'_groups'}->{$groupname} = [] if $groupname;
        while ( /^([a-z]\w+) +(.+)$/mg ) {
            #print "$1\t$2 \n" if $1;
            $self->{'_programs'}->{$1} = $2 if $1;
            $self->{'_programgroup'}->{$1} = $groupname if $1;
            push @{$self->{'_groups'}->{$groupname}}, $1 if $1;