diff variant_effect_predictor/Bio/AnalysisParserI.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/AnalysisParserI.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,195 @@
+#---------------------------------------------------------------
+# $Id: AnalysisParserI.pm,v 1.7 2002/12/01 00:05:19 jason Exp $
+#
+# BioPerl module Bio::AnalysisParserI
+#
+# Cared for by Steve Chervitz <[e-mail]>
+#
+# Derived from Bio::SeqAnalysisParserI by Jason Stajich, Hilmar Lapp.
+#
+# You may distribute this module under the same terms as perl itself
+#---------------------------------------------------------------
+
+=head1 NAME
+
+Bio::AnalysisParserI - Generic analysis output parser interface
+
+=head1 SYNOPSIS
+
+    # get a AnalysisParserI somehow.
+    # Eventually, there may be an Bio::Factory::AnalysisParserFactory.
+    # For now a SearchIO object, an implementation of AnalysisParserI, can be created 
+    # directly, as in the following:
+    my $parser = Bio::SearchIO->new(
+				    '-file'   => 'inputfile',
+				    '-format' => 'blast'); 
+
+    while( my $result = $parser->next_result() ) {
+	print "Result:  ", $result->analysis_method, 
+              ", Query:  ", $result->query_name, "\n";
+
+          while( my $feature = $result->next_feature() ) {
+              print "Feature from ", $feature->start, " to ", 
+                    $feature->end, "\n";
+          }
+    }
+
+=head1 DESCRIPTION
+
+AnalysisParserI is a interface for describing generic analysis
+result parsers. This module makes no assumption about the nature of
+analysis being parsed, only that zero or more result sets can be
+obtained from the input source.
+
+This module was derived from Bio::SeqAnalysisParserI, the differences being
+
+=over 4
+
+=item 1. next_feature() was replaced with next_result().
+
+Instead of flattening a stream containing potentially multiple
+analysis results into a single set of features, AnalysisParserI
+segments the stream in terms of analysis result sets
+(Bio::AnalysisResultI objects). Each AnalysisResultI can then be
+queried for its features (if any) as well as other information
+about the result
+
+=item 2. AnalysisParserI is a pure interface.
+
+It does not inherit from Bio::Root::RootI and does not provide a new()
+method. Implementations are free to choose how to implement it.
+
+=back
+
+=head2 Rationale (copied from Bio::SeqAnalysisParserI)
+
+The concept behind this interface is to have a generic interface in sequence
+annotation pipelines (as used e.g. in high-throughput automated
+sequence annotation). This interface enables plug-and-play for new analysis
+methods and their corresponding parsers without the necessity for modifying
+the core of the annotation pipeline. In this concept the annotation pipeline
+has to rely on only a list of methods for which to process the results, and a
+factory from which it can obtain the corresponding parser implementing this
+interface.
+
+=head2 TODO
+
+Create Bio::Factory::AnalysisParserFactoryI and
+Bio::Factory::AnalysisParserFactory for interface and an implementation.
+Note that this factory could return Bio::SearchIO-derived objects.
+
+=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 - Steve Chervitz, Jason Stajich, Hilmar Lapp
+
+Email [e-mail]
+
+Authors of Bio::SeqAnalysisParserI on which this module is based:
+Email [e-mail] 
+Email [e-mail]
+
+=head1 COPYRIGHT
+
+Copyright (c) 2001 Steve Chervitz. All Rights Reserved.
+
+=head1 DISCLAIMER
+
+This software is provided "as is" without warranty of any kind.
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object methods.
+Internal methods are usually preceded with a _
+
+=cut
+
+package Bio::AnalysisParserI;
+use strict;
+use vars qw(@ISA);
+
+use Bio::Root::RootI;
+
+@ISA = qw(Bio::Root::RootI);
+
+=head2 next_result
+
+ Title   : next_result
+ Usage   : $result = $obj->next_result();
+ Function: Returns the next result available from the input, or
+           undef if there are no more results.
+ Example :
+ Returns : A Bio::Search::Result::ResultI implementing object, 
+           or undef if there are no more results.
+ Args    : none
+
+=cut
+
+sub next_result {
+    my ($self);
+    $self->throw_not_implemented;
+}
+
+
+
+=head2 result_factory
+
+ Title   : result_factory
+ Usage   : $res_fact = $obj->result_factory;     (get)
+         : $obj->result_factory( $factory );      (set)
+ Function: Sets/Gets a factory object to create result objects for this AnalysisParser.
+ Returns : Bio::Factory::ResultFactoryI object 
+ Args    : Bio::Factory::ResultFactoryI object (when setting)
+ Comments: A AnalysisParserI implementation should provide a default result factory.
+           obtainable by the  default_result_factory_class() method.
+
+=cut
+
+sub result_factory {
+  my $self = shift;
+  $self->throw_not_implemented;
+}
+
+=head2 default_result_factory_class
+
+ Title   : default_result_factory_class
+ Usage   : $res_factory = $obj->default_result_factory_class()->new( @args )
+ Function: Returns the name of the default class to be used for creating
+           Bio::AnalysisResultI objects.
+ Example :
+ Returns : A string containing the name of a class that implements 
+           the Bio::Factory::ResultFactoryI interface.
+ Args    : none
+
+=cut
+
+sub default_result_factory_class {
+  my $self = shift;
+# TODO: Uncomment this when Jason's SearchIO code conforms
+#  $self->throw_not_implemented;
+}
+
+1;
+__END__
+
+NOTE: My ten-month old son Russell added the following line.
+It doesn't look like it will compile so I'm putting it here:
+mt6 j7qa