Summary

Bio::Tools::AlignFactory - Base object for alignment factories

Package variables

Included modules

Inherit

Bio::Root::Root

Synopsis

You wont be using this as an object, but using a dervied class
like Bio::Tools::pSW

Description

Holds common Alignment Factory attributes in place

Methods

Methods description

 Title     : kbyte()
 Usage     : set/gets the amount of memory able to be used
 Function  : 
           : $factory->kbyte(200);
           :
 Returns   : 
 Argument  : memory in kilobytes

 Title     : report()
 Usage     : set/gets the report boolean to issue reports or not
 Function  : 
           : $factory->report(1); # reporting goes on
           :
 Returns   : n/a
 Argument  : 1 or 0

 Title   : set_memory_and_report
 Usage   : Only used by subclasses.
 Function:
 Example :
 Returns : 
 Args    :

Methods code

BEGIN {

    eval {
	require Bio::Ext::Align;
    };
    if ( $@ ) {
	print STDERR ("\nThe C-compiled engine for Smith Waterman alignments (Bio::Ext::Align) has not been installed.\n Please install the bioperl-ext package\n\n");
	exit(1);

}

sub new {

  my($class,@args) = @_;
  my $self = $class->SUPER::new(@args);
  $self->_initialize(@args);
  # set up defaults
  
  $self->{'kbyte'} = 20000;
  $self->{'report'} = 0;  
  return $self;

}

sub kbyte {

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

}

sub report {

    my ($self,$value) = @_;
    

    if( defined $value ) {
	if( $value != 1 && $value != 0 ) {
	    $self->throw("Attempting to modify AlignFactory Report with no boolean value!");
	}
	$self->{'report'} = $value;
    } 

    return $self->{'report'};

}

sub set_memory_and_report {

   my ($self) = @_;

   if( $self->{'kbyte'} < 5 ) {
       $self->throw("You can suggest aligning things with less than 5kb");
   }

   &Bio::Ext::Align::change_max_BaseMatrix_kbytes($self->{'kbyte'});

   if( $self->{'report'} == 0 ) {
       &Bio::Ext::Align::error_off(16);
   } else {
       &Bio::Ext::Align::error_on(16);
   }

}

General documentation

http://bio.perl.org/ or birney@sanger.ac.uk

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