Bio/Search/Hit/Fasta.pm

   1 #
   2 # BioPerl module for Bio::Search::Hit::Fasta
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Aaron Mackey <amackey@virginia.edu>
   7 #
   8 # Copyright Aaron Mackey
   9 #
  10 # You may distribute this module under the same terms as perl itself
  11
  12 # POD documentation - main docs before the code
  13
  14 =head1 NAME
  15
  16 Bio::Search::Hit::Fasta - Hit object specific for Fasta-generated hits
  17
  18 =head1 SYNOPSIS
  19
  20   # You wouldn't normally create these manually;
  21   # instead they would be produced by Bio::SearchIO::fasta
  22
  23   use Bio::Search::Hit::Fasta;
  24   my $hit = Bio::Search::Hit::Fasta->new(id=>'LBL_6321', desc=>'lipoprotein', e_val=>0.01);
  25
  26 =head1 DESCRIPTION
  27
  28 L<Bio::Search::Hit::HitI> objects are data structures that contain information
  29 about specific hits obtained during a library search.  Some information will
  30 be algorithm-specific, but others will be generally defined, such as the
  31 ability to obtain alignment objects corresponding to each hit.
  32
  33 =head1 SEE ALSO
  34
  35 L<Bio::Search::Hit::HitI>,
  36 L<Bio::Search::Hit::GenericHit>,
  37 L<Bio::SearchIO::fasta>.
  38
  39 =head1 FEEDBACK
  40
  41 =head2 Mailing Lists
  42
  43 User feedback is an integral part of the evolution of this
  44 and other Bioperl modules. Send your comments and suggestions preferably
  45  to one of the Bioperl mailing lists.
  46 Your participation is much appreciated.
  47
  48   bioperl-l@bioperl.org                  - General discussion
  49   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  50
  51 =head2 Support
  52
  53 Please direct usage questions or support issues to the mailing list:
  54
  55 I<bioperl-l@bioperl.org>
  56
  57 rather than to the module maintainer directly. Many experienced and
  58 reponsive experts will be able look at the problem and quickly
  59 address it. Please include a thorough description of the problem
  60 with code and data examples if at all possible.
  61
  62 =head2 Reporting Bugs
  63
  64 Report bugs to the Bioperl bug tracking system to help us keep track
  65 the bugs and their resolution.  Bug reports can be submitted via the
  66 web:
  67
  68   https://github.com/bioperl/bioperl-live/issues
  69
  70 =head1 AUTHOR - Aaron Mackey
  71
  72 Email amackey-at-virginia.edu
  73
  74 =head1 APPENDIX
  75
  76 The rest of the documentation details each of the object
  77 methods. Internal methods are usually preceded with a _
  78
  79 =cut
  80
  81 #'
  82 # Let the code begin...
  83
  84 package Bio::Search::Hit::Fasta;
  85
  86 use vars qw($AUTOLOAD);
  87 use strict;
  88
  89 use base qw(Bio::Search::Hit::HitI);
  90
  91 my @AUTOLOAD_OK = qw(_ID _DESC _SIZE _INITN _INIT1 _OPT _ZSC _E_VAL);
  92
  93 my %AUTOLOAD_OK = ();
  94 @AUTOLOAD_OK{@AUTOLOAD_OK} = (1) x @AUTOLOAD_OK;
  95
  96 =head2 _initialize
  97
  98  Function: where the heavy stuff will happen when new is called
  99
 100 =cut
 101
 102 sub _initialize {
 103     my($self, %args) = @_;
 104
 105     my $make = $self->SUPER::_initialize(%args);
 106
 107     while (my ($key, $val) = each %args) {
 108         $key = '_' . uc($key);
 109         $self->$key($val);
 110     }
 111
 112     return $make; # success - we hope!
 113 }
 114
 115 =head2 AUTOLOAD
 116
 117  Function: Provide getter/setters for ID,DESC,SIZE,INITN,INIT1,OPT,ZSC,E_VAL
 118
 119 =cut
 120
 121 sub AUTOLOAD {
 122     my ($self, $val) = @_;
 123
 124     $AUTOLOAD =~ s/.*:://;
 125
 126     if ( $AUTOLOAD_OK{$AUTOLOAD} ) {
 127         $self->{$AUTOLOAD} = $val if defined $val;
 128         return $self->{$AUTOLOAD};
 129     } else {
 130         $self->throw("Unallowed accessor: $AUTOLOAD !");
 131     }
 132 }
 133
 134 1;
 135