Bio/Search/Hit/Fasta.pm

   1
   2 #
   3 # BioPerl module for Bio::Search::Hit::Fasta
   4 #
   5 # Cared for by Aaron Mackey <amackey@virginia.edu>
   6 #
   7 # Copyright Aaron Mackey
   8 #
   9 # You may distribute this module under the same terms as perl itself
  10
  11 # POD documentation - main docs before the code
  12
  13 =head1 NAME
  14
  15 Bio::Search::Hit::Fasta - Hit object specific for Fasta-generated hits
  16
  17 =head1 SYNOPSIS
  18
  19     These objects are generated automatically by Bio::Search::Processor::Fasta,
  20 and shouldn't be used directly.
  21
  22
  23 =head1 DESCRIPTION
  24
  25     Bio::Search::Hit::* objects are data structures that contain information
  26 about specific hits obtained during a library search.  Some information will
  27 be algorithm-specific, but others will be generally defined, such as the
  28 ability to obtain alignment objects corresponding to each hit.
  29
  30 =head1 FEEDBACK
  31
  32 =head2 Mailing Lists
  33
  34 User feedback is an integral part of the evolution of this
  35 and other Bioperl modules. Send your comments and suggestions preferably
  36  to one of the Bioperl mailing lists.
  37 Your participation is much appreciated.
  38
  39   bioperl-l@bioperl.org             - General discussion
  40   http://bio.perl.org/MailList.html - About the mailing lists
  41
  42 =head2 Reporting Bugs
  43
  44 Report bugs to the Bioperl bug tracking system to help us keep track
  45 the bugs and their resolution.  Bug reports can be submitted via email
  46 or the web:
  47
  48   bioperl-bugs@bio.perl.org
  49   http://bugzilla.bioperl.org/
  50
  51 =head1 AUTHOR - Aaron Mackey
  52
  53 Email amackey@virginia.edu
  54
  55 =head1 APPENDIX
  56
  57 The rest of the documentation details each of the object
  58 methods. Internal methods are usually preceded with a _
  59
  60 =cut
  61
  62 #'
  63 # Let the code begin...
  64
  65 package Bio::Search::Hit::Fasta;
  66
  67 use vars qw($AUTOLOAD @ISA);
  68 use strict;
  69
  70 # Object preamble - inherits from Bio::Root::Object
  71
  72 use Bio::Search::Hit::HitI;
  73
  74 @ISA = qw(Bio::Search::Hit::HitI);
  75
  76 my @AUTOLOAD_OK = qw(        _ID
  77                              _DESC
  78                              _SIZE
  79                              _INITN
  80                              _INIT1
  81                              _OPT
  82                              _ZSC
  83                              _E_VAL
  84                     );
  85
  86 my %AUTOLOAD_OK = ();
  87 @AUTOLOAD_OK{@AUTOLOAD_OK} = (1) x @AUTOLOAD_OK;
  88
  89 # new() is inherited from Bio::Root::Object
  90
  91 # _initialize is where the heavy stuff will happen when new is called
  92
  93 sub _initialize {
  94     my($self, %args) = @_;
  95
  96     my $make = $self->SUPER::_initialize(%args);
  97
  98     while (my ($key, $val) = each %args) {
  99         $key = '_' . uc($key);
 100         $self->$key($val);
 101     }
 102
 103     return $make; # success - we hope!
 104 }
 105
 106 sub AUTOLOAD {
 107     my ($self, $val) = @_;
 108
 109     $AUTOLOAD =~ s/.*:://;
 110
 111     if ( $AUTOLOAD_OK{$AUTOLOAD} ) {
 112         $self->{$AUTOLOAD} = $val if defined $val;
 113         return $self->{$AUTOLOAD};
 114     } else {
 115         $self->throw("Unallowed accessor: $AUTOLOAD !");
 116     }
 117 }
 118
 119 1;
 120
 121 __END__