diff variant_effect_predictor/Bio/Search/Hit/Fasta.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Search/Hit/Fasta.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,121 @@
+
+#
+# BioPerl module for Bio::Search::Hit::Fasta
+#
+# 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::Hit::Fasta - Hit object specific for Fasta-generated hits
+
+=head1 SYNOPSIS
+
+    These objects are generated automatically by Bio::Search::Processor::Fasta,
+and shouldn't be used directly.
+
+
+=head1 DESCRIPTION
+
+    Bio::Search::Hit::* objects are data structures that contain information
+about specific hits obtained during a library search.  Some information will
+be algorithm-specific, but others will be generally defined, such as the
+ability to obtain alignment objects corresponding to each hit.
+
+=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]
+
+=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::Hit::Fasta;
+
+use vars qw($AUTOLOAD @ISA);
+use strict;
+
+# Object preamble - inherits from Bio::Root::Object
+
+use Bio::Search::Hit::HitI;
+
+@ISA = qw(Bio::Search::Hit::HitI);
+
+my @AUTOLOAD_OK = qw(        _ID
+                             _DESC
+                             _SIZE
+                             _INITN
+                             _INIT1
+                             _OPT
+                             _ZSC
+                             _E_VAL
+                    );
+
+my %AUTOLOAD_OK = ();
+@AUTOLOAD_OK{@AUTOLOAD_OK} = (1) x @AUTOLOAD_OK;
+
+# new() is inherited from Bio::Root::Object
+
+# _initialize is where the heavy stuff will happen when new is called
+
+sub _initialize {
+    my($self, %args) = @_;
+
+    my $make = $self->SUPER::_initialize(%args);
+
+    while (my ($key, $val) = each %args) {
+	$key = '_' . uc($key);
+	$self->$key($val);
+    }
+
+    return $make; # success - we hope!
+}
+
+sub AUTOLOAD {
+    my ($self, $val) = @_;
+
+    $AUTOLOAD =~ s/.*:://;
+
+    if ( $AUTOLOAD_OK{$AUTOLOAD} ) {
+        $self->{$AUTOLOAD} = $val if defined $val;
+        return $self->{$AUTOLOAD};
+    } else {
+        $self->throw("Unallowed accessor: $AUTOLOAD !");
+    }
+}
+
+1;
+
+__END__