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lib/Bio/Tools/Run/Alignment/MSAProbs.pm  view on Meta::CPAN

    if( defined($input) ) {
	$infilename = $self->_setinput($input);
    } elsif( defined($self->infile) ) {
	$infilename = $self->_setinput($self->infile);
    } else {
	$self->throw("No inputdata provided\n");
    }
    unless( $infilename ) {
	$self->throw("Bad input data or less than 2 sequences in $infilename !");
    }
    
    my $param_string = $self->_setparams();

    # run msaprobs
    return &_run($self, $infilename, $param_string);
}

=head2 error_string

 Title   : error_string
 Usage   : $obj->error_string($newval)
 Function: Where the output from the last analysus run is stored.
 Returns : value of error_string
 Args    : newvalue (optional)


=cut

sub error_string{
   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'error_string'} = $value;
    }
    return $self->{'error_string'};

}

=head2  infile

 Title   : infile
 Usage   : $prog->infile($filename)
 Function: get/set the fasta (and only a fasta) file to run on
           or the array reference containing the Bio::SeqI objects
 Returns : name of input sequence file or object array ref
 Args    : name of input sequence file or object array ref

 
=cut

=head2  outfile

 Title   : outfile
 Usage   : $prog->outfile($filename)
 Function: get/set the file to save output to
 Returns : outfile name if set
 Args    : newvalue (optional)

 
=cut

=head2  annot_file

 Title   : annot_file
 Usage   : $prog->annot_file($filename)
 Function: get/set the file name to write the MSA annotation to
 Returns : filename or undef
 Args    : filename (optional)

 
=cut

=head2  num_threads

 Title   : num_threads
 Usage   : $prog->num_threads($cores)
 Function: get/set number of cores on your machine
 Returns : integer
 Args    : integer (optional; executable auto-detects)

 
=cut

=head2  consistency

 Title   : consistency
 Usage   : $prog->consistency($passes)
 Function: get/set the number of consistency transformation passes
 Returns : integer
 Args    : integer 0..5, [default 2] (optional)

 
=cut

=head2  iterations

 Title   : iterations
 Usage   : $prog->iterations($passes)
 Function: get/set the number of iterative-refinement passes
 Returns : integer
 Args    : integer 0..1000, [default 10] (optional)

 
=cut

=head2  alignment_order

 Title   : alignment_order
 Usage   : $prog->alignment_order($bool)
 Function: specify whether or not to output aligned sequences in
           alignment order, not input order
 Returns : boolean
 Args    : boolean [default: off] (optional)

 
=cut

=head2  clustalw

 Title   : clustalw
 Usage   : $prog->clustalw($bool)
 Function: write output in clustalw format; makes no sense unless
           outfile() is also specified
 Returns : boolean
 Args    : boolean [default: off] (optional)