diff variant_effect_predictor/Bio/Search/Processor.pm @ 0:21066c0abaf5 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Search/Processor.pm	Fri Aug 03 10:04:48 2012 -0400
@@ -0,0 +1,115 @@
+
+#
+# BioPerl module for Bio::Search::Processor
+#
+# Cared for by Aaron Mackey <[e-mail]>
+#
+# Copyright Aaron Mackey
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Search::Processor - DESCRIPTION of Object
+
+=head1 SYNOPSIS
+
+Give standard usage here
+
+=head1 DESCRIPTION
+
+Describe the object here
+
+=head1 FEEDBACK
+
+=head2 Mailing Lists
+
+User feedback is an integral part of the evolution of this and other
+Bioperl modules. Send your comments and suggestions preferably to one
+of the Bioperl mailing lists.  Your participation is much appreciated.
+
+  [e-mail]              - General discussion
+  http://bio.perl.org/MailList.html  - About the mailing lists
+
+=head2 Reporting Bugs
+
+Report bugs to the Bioperl bug tracking system to help us keep track
+the bugs and their resolution.  Bug reports can be submitted via email
+or the web:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR - Aaron Mackey
+
+Email [e-mail]
+
+Describe contact details here
+
+=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::Search::Processor;
+
+use strict;
+use vars qw(@ISA);
+
+=head2 new
+
+ Title   : new
+ Usage   : $proc = new Bio::Search::Processor -file      => $filename,
+                                              -algorithm => 'Algorithm' ;
+ Function: Used to specify and initialize a data processor of search
+           algorithm results.
+ Returns : A processor specific to the algorithm type, if it exists.
+ Args    : -file => filename
+           -algorithm => algorithm specifier
+           -fh => filehandle to attach to (file or fh required)
+
+=cut
+
+sub new {
+
+    my $type = shift;
+    my $proc;
+    my ($module, $load, $algorithm);
+
+    my %args = @_;
+
+    exists $args{'-algorithm'} or do { 
+	print STDERR "Must supply an algorithm!";
+	return undef;
+    };
+
+    $algorithm = $args{'-algorithm'} || $args{'-ALGORITHM'};
+
+    $module = "_<Bio/Search/Processor/$algorithm.pm";
+    $load = "Bio/Search/Processor/$algorithm.pm";
+
+    unless ( $main::{$module} ) {
+	eval { require $load; };
+	if ( $@ ) {
+	    print STDERR <<"EOF";
+$load: $algorithm cannot be found
+Exception $@
+For more information about the Search/Processor system please see the
+Processor docs.  This includes ways of checking for processors at 
+compile time, not run time
+EOF
+	    return undef;
+	}
+    }
+
+    $proc = "Bio::Search::Processor::$algorithm"->new(@_);
+    return $proc;
+}
+
+1;