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1 # $Id: AlignFactory.pm,v 1.8 2001/11/20 02:09:40 lstein Exp $
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2 #
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3 # BioPerl module for Bio::Tools::AlignFactory
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4 #
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5 # Cared for by Ewan Birney <birney@sanger.ac.uk>
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6 #
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7 # Copyright Ewan Birney
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8 #
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9 # You may distribute this module under the same terms as perl itself
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10
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11 # POD documentation - main docs before the code
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12
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13 =head1 NAME
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14
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15 Bio::Tools::AlignFactory - Base object for alignment factories
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16
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17 =head1 SYNOPSIS
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18
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19 You wont be using this as an object, but using a dervied class
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20 like Bio::Tools::pSW
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21
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22 =head1 DESCRIPTION
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23
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24 Holds common Alignment Factory attributes in place
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25
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26 =head1 CONTACT
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27
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28 http://bio.perl.org/ or birney@sanger.ac.uk
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29
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30 =head1 APPENDIX
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31
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32 The rest of the documentation details each of the object
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33 methods. Internal methods are usually preceded with a _
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34
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35 =cut
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36
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37
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38 # Let the code begin...
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39
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40 package Bio::Tools::AlignFactory;
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41 use vars qw(@ISA);
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42 use strict;
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43
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44 use Bio::Root::Root;
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45 @ISA = qw(Bio::Root::Root);
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46
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47 BEGIN {
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48 eval {
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49 require Bio::Ext::Align;
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50 };
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51 if ( $@ ) {
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52 print STDERR ("\nThe C-compiled engine for Smith Waterman alignments (Bio::Ext::Align) has not been installed.\n Please install the bioperl-ext package\n\n");
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53 exit(1);
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54 }
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55 }
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56
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57 sub new {
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58 my($class,@args) = @_;
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59 my $self = $class->SUPER::new(@args);
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60 $self->_initialize(@args);
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61 # set up defaults
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62
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63 $self->{'kbyte'} = 20000;
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64 $self->{'report'} = 0;
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65 return $self;
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66 }
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67
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68
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69 =head2 kbyte
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70
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71 Title : kbyte()
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72 Usage : set/gets the amount of memory able to be used
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73 Function :
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74 : $factory->kbyte(200);
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75 :
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76 Returns :
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77 Argument : memory in kilobytes
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78
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79 =cut
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80
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81 sub kbyte {
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82 my ($self,$value) = @_;
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83
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84 if( defined $value ) {
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85 $self->{'kbyte'} = $value;
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86 }
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87 return $self->{'kbyte'};
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88 }
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89
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90
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91 =head2 report
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92
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93 Title : report()
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94 Usage : set/gets the report boolean to issue reports or not
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95 Function :
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96 : $factory->report(1); # reporting goes on
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97 :
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98 Returns : n/a
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99 Argument : 1 or 0
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100
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101 =cut
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102
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103 sub report {
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104 my ($self,$value) = @_;
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105
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106
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107 if( defined $value ) {
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108 if( $value != 1 && $value != 0 ) {
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109 $self->throw("Attempting to modify AlignFactory Report with no boolean value!");
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110 }
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111 $self->{'report'} = $value;
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112 }
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113
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114 return $self->{'report'};
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115 }
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116
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117 =head2 set_memory_and_report
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118
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119 Title : set_memory_and_report
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120 Usage : Only used by subclasses.
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121 Function:
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122 Example :
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123 Returns :
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124 Args :
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125
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126
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127 =cut
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128
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129 sub set_memory_and_report{
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130 my ($self) = @_;
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131
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132 if( $self->{'kbyte'} < 5 ) {
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133 $self->throw("You can suggest aligning things with less than 5kb");
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134 }
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135
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136 &Bio::Ext::Align::change_max_BaseMatrix_kbytes($self->{'kbyte'});
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137
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138 if( $self->{'report'} == 0 ) {
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139 &Bio::Ext::Align::error_off(16);
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140 } else {
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141 &Bio::Ext::Align::error_on(16);
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142 }
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143 }
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144
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145 1;
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