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1 # $Id: SeqAnalysisParserFactoryI.pm,v 1.8 2002/12/01 00:05:20 jason Exp $
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2 #
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3 # BioPerl module for Bio::Factory::SeqAnalysisParserFactoryI
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4 #
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5 # Cared for by Jason Stajich <jason@bioperl.org>,
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6 # and Hilmar Lapp <hlapp@gmx.net>
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7 #
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8 # Copyright Jason Stajich, Hilmar Lapp
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9 #
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10 # You may distribute this module under the same terms as perl itself
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11
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12 # POD documentation - main docs before the code
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13
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14 =head1 NAME
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15
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16 Bio::Factory::SeqAnalysisParserFactoryI - interface describing objects capable
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17 of creating SeqAnalysisParserI compliant parsers
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18
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19 =head1 SYNOPSIS
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20
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21 # initialize an object implementing this interface, e.g.
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22 $factory = Bio::Factory::SeqAnalysisParserFactory->new();
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23 # obtain a parser object
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24 $parser = $factory->get_parser(-input=>$inputobj,
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25 -params=>[@params],
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26 -method => $method);
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27 # $parser is an object implementing Bio::SeqAnalysisParserI
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28 # annotate sequence with features produced by parser
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29 while(my $feat = $parser->next_feature()) {
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30 $seq->add_SeqFeature($feat);
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31 }
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32
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33 =head1 DESCRIPTION
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34
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35 This is an interface for factory classes capable of instantiating
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36 SeqAnalysisParserI implementing parsers.
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37
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38 The concept behind the interface is a generic analysis result parsing
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39 in high-throughput automated sequence annotation pipelines. See
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40 L<Bio::SeqAnalysisParserI> for more documentation of this concept.
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41
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42 =head1 FEEDBACK
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43
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44 =head2 Mailing Lists
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45
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46 User feedback is an integral part of the evolution of this
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47 and other Bioperl modules. Send your comments and suggestions preferably
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48 to one of the Bioperl mailing lists.
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49 Your participation is much appreciated.
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50
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51 bioperl-l@bioperl.org - General discussion
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52 http://bio.perl.org/MailList.html - About the mailing lists
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53
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54 =head2 Reporting Bugs
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55
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56 Report bugs to the Bioperl bug tracking system to help us keep track
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57 the bugs and their resolution.
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58 Bug reports can be submitted via email or the web:
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59
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60 bioperl-bugs@bio.perl.org
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61 http://bugzilla.bioperl.org/
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62
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63 =head1 AUTHOR - Hilmar Lapp, Jason Stajich
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64
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65 Email Hilmar Lapp E<lt>hlapp@gmx.netE<gt>, Jason Stajich E<lt>jason@bioperl.orgE<gt>
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66
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67 =head1 APPENDIX
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68
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69 The rest of the documentation details each of the object
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70 methods. Internal methods are usually preceded with a _
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71
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72 =cut
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73
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74 package Bio::Factory::SeqAnalysisParserFactoryI;
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75 use strict;
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76
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77 use Bio::Root::RootI;
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78 use Carp;
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79
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80 use vars qw(@ISA );
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81 @ISA = qw(Bio::Root::RootI);
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82
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83 =head2 get_parser
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84
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85 Title : get_parser
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86 Usage : $factory->get_parser(-input=>$inputobj,
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87 [ -params=>[@params] ],
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88 -method => $method)
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89 Function: Creates and returns a parser object for the given input and method.
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90 The type of input which is suitable depends on the implementation,
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91 but a good-style implementation should allow both file names and
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92 streams (filehandles).
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93
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94 A particular implementation may not be able to create a parser for
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95 the requested method. In this case it shall return undef.
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96
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97 Parameters (-params argument) are passed on to the parser object
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98 and therefore are specific to the parser to be created. An
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99 implementation of this interface should make this argument optional.
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100 Example :
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101 Returns : A Bio::SeqAnalysisParserI implementing object.
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102 Args : B<input> - object/file where analysis results are coming from,
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103 B<params> - parameter to use when parsing/running analysis
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104 B<method> - method of analysis
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105
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106 =cut
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107
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108 sub get_parser {
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109 my ( $self, @args) = @_;
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110 $self->throw_not_implemented();
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111 }
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112
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113 1;
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