3 # BioPerl module for Bio::Search::Hit::Fasta
5 # Cared for by Aaron Mackey <amackey@virginia.edu>
7 # Copyright Aaron Mackey
9 # You may distribute this module under the same terms as perl itself
11 # POD documentation - main docs before the code
15 Bio::Search::Hit::Fasta - Hit object specific for Fasta-generated hits
19 These objects are generated automatically by Bio::Search::Processor::Fasta,
20 and shouldn't be used directly.
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.
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.
39 bioperl-l@bioperl.org - General discussion
40 http://bio.perl.org/MailList.html - About the mailing lists
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
48 bioperl-bugs@bio.perl.org
49 http://bugzilla.bioperl.org/
51 =head1 AUTHOR - Aaron Mackey
53 Email amackey@virginia.edu
57 The rest of the documentation details each of the object
58 methods. Internal methods are usually preceded with a _
63 # Let the code begin...
65 package Bio
::Search
::Hit
::Fasta
;
67 use vars
qw($AUTOLOAD @ISA);
70 # Object preamble - inherits from Bio::Root::Object
72 use Bio::Search::Hit::HitI;
74 @ISA = qw(Bio::Search::Hit::HitI);
76 my @AUTOLOAD_OK = qw( _ID
87 @AUTOLOAD_OK{@AUTOLOAD_OK} = (1) x
@AUTOLOAD_OK;
89 # new() is inherited from Bio::Root::Object
91 # _initialize is where the heavy stuff will happen when new is called
94 my($self, %args) = @_;
96 my $make = $self->SUPER::_initialize
(%args);
98 while (my ($key, $val) = each %args) {
99 $key = '_' . uc($key);
103 return $make; # success - we hope!
107 my ($self, $val) = @_;
109 $AUTOLOAD =~ s/.*:://;
111 if ( $AUTOLOAD_OK{$AUTOLOAD} ) {
112 $self->{$AUTOLOAD} = $val if defined $val;
113 return $self->{$AUTOLOAD};
115 $self->throw("Unallowed accessor: $AUTOLOAD !");