Bio/Tools/AlignFactory.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::Tools::AlignFactory
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Ewan Birney <birney@sanger.ac.uk>
   8 #
   9 # Copyright Ewan Birney
  10 #
  11 # You may distribute this module under the same terms as perl itself
  12
  13 # POD documentation - main docs before the code
  14
  15 =head1 NAME
  16
  17 Bio::Tools::AlignFactory - Base object for alignment factories
  18
  19 =head1 SYNOPSIS
  20
  21 You wont be using this as an object, but using a dervied class
  22 like Bio::Tools::pSW
  23
  24 =head1 DESCRIPTION
  25
  26 Holds common Alignment Factory attributes in place
  27
  28 =head1 CONTACT
  29
  30 http://bio.perl.org/ or birney@sanger.ac.uk
  31
  32 =head1 APPENDIX
  33
  34 The rest of the documentation details each of the object
  35 methods. Internal methods are usually preceded with a _
  36
  37 =cut
  38
  39
  40 # Let the code begin...
  41
  42 package Bio::Tools::AlignFactory;
  43 use strict;
  44
  45 use base qw(Bio::Root::Root);
  46
  47 BEGIN {
  48     eval {
  49         require Bio::Ext::Align;
  50     };
  51     if ( $@ ) {
  52         print STDERR ("\nThe C-compiled engine for Smith Waterman alignments (Bio::Ext::Align) has not been installed.\n Please install the bioperl-ext package\n\n");
  53         exit(1);
  54     }
  55 }
  56
  57 sub new {
  58   my($class,@args) = @_;
  59   my $self = $class->SUPER::new(@args);
  60   $self->_initialize(@args);
  61   # set up defaults
  62
  63   $self->{'kbyte'} = 20000;
  64   $self->{'report'} = 0;
  65   return $self;
  66 }
  67
  68
  69 =head2 kbyte
  70
  71  Title     : kbyte()
  72  Usage     : set/gets the amount of memory able to be used
  73  Function  :
  74            : $factory->kbyte(200);
  75            :
  76  Returns   :
  77  Argument  : memory in kilobytes
  78
  79 =cut
  80
  81 sub kbyte {
  82     my ($self,$value) = @_;
  83
  84     if( defined $value ) {
  85         $self->{'kbyte'} = $value;
  86     }
  87     return $self->{'kbyte'};
  88 }
  89
  90
  91 =head2 report
  92
  93  Title     : report()
  94  Usage     : set/gets the report boolean to issue reports or not
  95  Function  :
  96            : $factory->report(1); # reporting goes on
  97            :
  98  Returns   : n/a
  99  Argument  : 1 or 0
 100
 101 =cut
 102
 103 sub report {
 104     my ($self,$value) = @_;
 105
 106
 107     if( defined $value ) {
 108         if( $value != 1 && $value != 0 ) {
 109             $self->throw("Attempting to modify AlignFactory Report with no boolean value!");
 110         }
 111         $self->{'report'} = $value;
 112     }
 113
 114     return $self->{'report'};
 115 }
 116
 117 =head2 set_memory_and_report
 118
 119  Title   : set_memory_and_report
 120  Usage   : Only used by subclasses.
 121  Function:
 122  Example :
 123  Returns :
 124  Args    :
 125
 126
 127 =cut
 128
 129 sub set_memory_and_report{
 130    my ($self) = @_;
 131
 132    if( $self->{'kbyte'} < 5 ) {
 133        $self->throw("You can suggest aligning things with less than 5kb");
 134    }
 135
 136    &Bio::Ext::Align::change_max_BaseMatrix_kbytes($self->{'kbyte'});
 137
 138    if( $self->{'report'} == 0 ) {
 139        &Bio::Ext::Align::error_off(16);
 140    } else {
 141        &Bio::Ext::Align::error_on(16);
 142    }
 143 }
 144
 145 1;