Bio/Tools/AlignFactory.pm

   1
   2 #
   3 # BioPerl module for Bio::Tools::AlignFactory
   4 #
   5 # Cared for by Ewan Birney <birney@sanger.ac.uk>
   6 #
   7 # Copyright Ewan Birney
   8 #
   9 # You may distribute this module under the same terms as perl itself
  10
  11 # POD documentation - main docs before the code
  12
  13 =head1 NAME
  14
  15 Bio::Tools::AlignFactory - Base object for alignment factories
  16
  17 =head1 SYNOPSIS
  18
  19 You wont be using this as an object, but using a dervied class
  20 like Bio::Tools::pSW
  21
  22 =head1 DESCRIPTION
  23
  24 Holds common Alignment Factory attributes in place
  25
  26 =head1 CONTACT
  27
  28 http://bio.perl.org/ or birney@sanger.ac.uk
  29
  30 =head1 APPENDIX
  31
  32 The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
  33
  34 =cut
  35
  36
  37 # Let the code begin...
  38
  39
  40 package Bio::Tools::AlignFactory;
  41 use vars qw($AUTOLOAD @ISA);
  42 use strict;
  43
  44 # Object preamble - inheriets from Bio::Root::Object
  45
  46 use Bio::Root::Object;
  47
  48 BEGIN {
  49     eval {
  50         require Bio::Ext::Align;
  51     };
  52     if ( $@ ) {
  53         print STDERR ("\nThe C-compiled engine for Smith Waterman alignments (Bio::Ext::Align) has not been installed.\n Please install the bioperl-ext package\n\n");
  54         exit(1);
  55     }
  56 }
  57
  58
  59 @ISA = qw(Bio::Root::Object Exporter);
  60 # new() is inherited from Bio::Root::Object
  61
  62 # _initialize is where the heavy stuff will happen when new is called
  63
  64 sub _initialize {
  65   my($self,@p) = @_;
  66   my $make = $self->SUPER::_initialize(@p);
  67
  68   # set up defaults
  69
  70   $self->{'kbyte'} = 20000;
  71   $self->{'report'} = 0;
  72 # set stuff in self from @args
  73  return $make; # success - we hope!
  74 }
  75
  76
  77 =head2 kbyte
  78
  79  Title     : kbyte()
  80  Usage     : set/gets the amount of memory able to be used
  81  Function  :
  82            : $factory->kbyte(200);
  83            :
  84  Returns   :
  85  Argument  : memory in kilobytes
  86
  87 =cut
  88
  89 sub kbyte {
  90     my ($self,$value) = @_;
  91
  92     if( defined $value ) {
  93         $self->{'kbyte'} = $value;
  94     }
  95
  96     return $self->{'kbyte'};
  97 }
  98
  99
 100 =head2 report
 101
 102  Title     : report()
 103  Usage     : set/gets the report boolean to issue reports or not
 104  Function  :
 105            : $factory->report(1); # reporting goes on
 106            :
 107  Returns   : n/a
 108  Argument  : 1 or 0
 109
 110 =cut
 111
 112 sub report {
 113     my ($self,$value) = @_;
 114
 115
 116     if( defined $value ) {
 117         if( $value != 1 && $value != 0 ) {
 118             $self->throw("Attempting to modify AlignFactory Report with no boolean value!");
 119         }
 120         $self->{'report'} = $value;
 121     }
 122
 123     return $self->{'report'};
 124 }
 125
 126 =head2 set_memory_and_report
 127
 128  Title   : set_memory_and_report
 129  Usage   : Only used by subclasses.
 130  Function:
 131  Example :
 132  Returns :
 133  Args    :
 134
 135
 136 =cut
 137
 138 sub set_memory_and_report{
 139    my ($self) = @_;
 140
 141    if( $self->{'kbyte'} < 5 ) {
 142        $self->throw("You can suggest aligning things with less than 5kb");
 143    }
 144
 145    &Bio::Ext::Align::change_max_BaseMatrix_kbytes($self->{'kbyte'});
 146
 147    if( $self->{'report'} == 0 ) {
 148        &bp_sw::error_off(16);
 149    } else {
 150        &bp_sw::error_on(16);
 151    }
 152 }
 153
 154
 155