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