diff variant_effect_predictor/Bio/Tools/AlignFactory.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Tools/AlignFactory.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,145 @@
+# $Id: AlignFactory.pm,v 1.8 2001/11/20 02:09:40 lstein Exp $
+#
+# BioPerl module for Bio::Tools::AlignFactory
+#
+# Cared for by Ewan Birney <[e-mail]>
+#
+# Copyright Ewan Birney
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Tools::AlignFactory - Base object for alignment factories
+
+=head1 SYNOPSIS
+
+You wont be using this as an object, but using a dervied class
+like Bio::Tools::pSW
+
+=head1 DESCRIPTION
+
+Holds common Alignment Factory attributes in place
+
+=head1 CONTACT
+
+http://bio.perl.org/ or [e-mail] 
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object
+methods. Internal methods are usually preceded with a _
+
+=cut
+
+
+# Let the code begin...
+
+package Bio::Tools::AlignFactory;
+use vars qw(@ISA);
+use strict;
+
+use Bio::Root::Root;
+@ISA = qw(Bio::Root::Root);
+
+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;
+}
+
+
+=head2 kbyte
+
+ Title     : kbyte()
+ Usage     : set/gets the amount of memory able to be used
+ Function  : 
+           : $factory->kbyte(200);
+           :
+ Returns   : 
+ Argument  : memory in kilobytes
+
+=cut
+
+sub kbyte {
+    my ($self,$value) = @_;
+    
+    if( defined $value ) {
+	$self->{'kbyte'} = $value;
+    } 
+    return $self->{'kbyte'};
+}
+
+
+=head2 report
+
+ Title     : report()
+ Usage     : set/gets the report boolean to issue reports or not
+ Function  : 
+           : $factory->report(1); # reporting goes on
+           :
+ Returns   : n/a
+ Argument  : 1 or 0
+
+=cut
+
+sub report {
+    my ($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 $self->{'report'};
+}
+
+=head2 set_memory_and_report
+
+ Title   : set_memory_and_report
+ Usage   : Only used by subclasses.
+ Function:
+ Example :
+ Returns : 
+ Args    :
+
+
+=cut
+
+sub set_memory_and_report{
+   my ($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);
+   }
+}
+
+1;