branch-1-6/Bio/Search/Hit/Fasta.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::Search::Hit::Fasta
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Aaron Mackey <amackey@virginia.edu>
   8 #
   9 # Copyright Aaron Mackey
  10 #
  11 # You may distribute this module under the same terms as perl itself
  12
  13 # POD documentation - main docs before the code
  14
  15 =head1 NAME
  16
  17 Bio::Search::Hit::Fasta - Hit object specific for Fasta-generated hits
  18
  19 =head1 SYNOPSIS
  20
  21   # You wouldn't normally create these manually;
  22   # instead they would be produced by Bio::SearchIO::fasta
  23
  24   use Bio::Search::Hit::Fasta;
  25   my $hit = Bio::Search::Hit::Fasta->new(id=>'LBL_6321', desc=>'lipoprotein', e_val=>0.01);
  26
  27 =head1 DESCRIPTION
  28
  29 L<Bio::Search::Hit::HitI> objects are data structures that contain information
  30 about specific hits obtained during a library search.  Some information will
  31 be algorithm-specific, but others will be generally defined, such as the
  32 ability to obtain alignment objects corresponding to each hit.
  33
  34 =head1 SEE ALSO
  35
  36 L<Bio::Search::Hit::HitI>,
  37 L<Bio::Search::Hit::GenericHit>,
  38 L<Bio::SearchIO::fasta>.
  39
  40 =head1 FEEDBACK
  41
  42 =head2 Mailing Lists
  43
  44 User feedback is an integral part of the evolution of this
  45 and other Bioperl modules. Send your comments and suggestions preferably
  46  to one of the Bioperl mailing lists.
  47 Your participation is much appreciated.
  48
  49   bioperl-l@bioperl.org                  - General discussion
  50   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  51
  52 =head2 Support
  53
  54 Please direct usage questions or support issues to the mailing list:
  55
  56 I<bioperl-l@bioperl.org>
  57
  58 rather than to the module maintainer directly. Many experienced and
  59 reponsive experts will be able look at the problem and quickly
  60 address it. Please include a thorough description of the problem
  61 with code and data examples if at all possible.
  62
  63 =head2 Reporting Bugs
  64
  65 Report bugs to the Bioperl bug tracking system to help us keep track
  66 the bugs and their resolution.  Bug reports can be submitted via the
  67 web:
  68
  69   http://bugzilla.open-bio.org/
  70
  71 =head1 AUTHOR - Aaron Mackey
  72
  73 Email amackey-at-virginia.edu
  74
  75 =head1 APPENDIX
  76
  77 The rest of the documentation details each of the object
  78 methods. Internal methods are usually preceded with a _
  79
  80 =cut
  81
  82 #'
  83 # Let the code begin...
  84
  85 package Bio::Search::Hit::Fasta;
  86
  87 use vars qw($AUTOLOAD);
  88 use strict;
  89
  90 use base qw(Bio::Search::Hit::HitI);
  91
  92 my @AUTOLOAD_OK = qw(_ID _DESC _SIZE _INITN _INIT1 _OPT _ZSC _E_VAL);
  93
  94 my %AUTOLOAD_OK = ();
  95 @AUTOLOAD_OK{@AUTOLOAD_OK} = (1) x @AUTOLOAD_OK;
  96
  97 =head2 _initialize
  98
  99  Function: where the heavy stuff will happen when new is called
 100
 101 =cut
 102
 103 sub _initialize {
 104     my($self, %args) = @_;
 105
 106     my $make = $self->SUPER::_initialize(%args);
 107
 108     while (my ($key, $val) = each %args) {
 109         $key = '_' . uc($key);
 110         $self->$key($val);
 111     }
 112
 113     return $make; # success - we hope!
 114 }
 115
 116 =head2 AUTOLOAD
 117
 118  Function: Provide getter/setters for ID,DESC,SIZE,INITN,INIT1,OPT,ZSC,E_VAL
 119
 120 =cut
 121
 122 sub AUTOLOAD {
 123     my ($self, $val) = @_;
 124
 125     $AUTOLOAD =~ s/.*:://;
 126
 127     if ( $AUTOLOAD_OK{$AUTOLOAD} ) {
 128         $self->{$AUTOLOAD} = $val if defined $val;
 129         return $self->{$AUTOLOAD};
 130     } else {
 131         $self->throw("Unallowed accessor: $AUTOLOAD !");
 132     }
 133 }
 134
 135 1;
 136