lib/Bio/Search/Processor.pm

   1
   2 #
   3 # BioPerl module for Bio::Search::Processor
   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::Processor - DESCRIPTION of Object
  18
  19 =head1 SYNOPSIS
  20
  21 Give standard usage here
  22
  23 =head1 DESCRIPTION
  24
  25 Describe the object here
  26
  27 =head1 FEEDBACK
  28
  29 =head2 Mailing Lists
  30
  31 User feedback is an integral part of the evolution of this and other
  32 Bioperl modules. Send your comments and suggestions preferably to one
  33 of the Bioperl mailing lists.  Your participation is much appreciated.
  34
  35   bioperl-l@bioperl.org                  - General discussion
  36   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  37
  38 =head2 Support
  39
  40 Please direct usage questions or support issues to the mailing list:
  41
  42 I<bioperl-l@bioperl.org>
  43
  44 rather than to the module maintainer directly. Many experienced and
  45 reponsive experts will be able look at the problem and quickly
  46 address it. Please include a thorough description of the problem
  47 with code and data examples if at all possible.
  48
  49 =head2 Reporting Bugs
  50
  51 Report bugs to the Bioperl bug tracking system to help us keep track
  52 the bugs and their resolution.  Bug reports can be submitted via the
  53 web:
  54
  55   https://github.com/bioperl/bioperl-live/issues
  56
  57 =head1 AUTHOR - Aaron Mackey
  58
  59 Email amackey@virginia.edu
  60
  61 Describe contact details here
  62
  63 =head1 APPENDIX
  64
  65 The rest of the documentation details each of the object
  66 methods. Internal methods are usually preceded with a _
  67
  68 =cut
  69
  70 # Let the code begin...
  71
  72 package Bio::Search::Processor;
  73
  74 use strict;
  75
  76 =head2 new
  77
  78  Title   : new
  79  Usage   : $proc = Bio::Search::Processor->new -file      => $filename,
  80                                               -algorithm => 'Algorithm' ;
  81  Function: Used to specify and initialize a data processor of search
  82            algorithm results.
  83  Returns : A processor specific to the algorithm type, if it exists.
  84  Args    : -file => filename
  85            -algorithm => algorithm specifier
  86            -fh => filehandle to attach to (file or fh required)
  87
  88 =cut
  89
  90 sub new {
  91
  92     my $type = shift;
  93     my $proc;
  94     my ($module, $load, $algorithm);
  95
  96     my %args = @_;
  97
  98     exists $args{'-algorithm'} or do {
  99         print STDERR "Must supply an algorithm!";
 100         return;
 101     };
 102
 103     $algorithm = $args{'-algorithm'} || $args{'-ALGORITHM'};
 104
 105     $module = "_<Bio/Search/Processor/$algorithm.pm";
 106     $load = "Bio/Search/Processor/$algorithm.pm";
 107
 108     unless ( $main::{$module} ) {
 109         eval { require $load; };
 110         if ( $@ ) {
 111             print STDERR <<"EOF";
 112 $load: $algorithm cannot be found
 113 Exception $@
 114 For more information about the Search/Processor system please see the
 115 Processor docs.  This includes ways of checking for processors at
 116 compile time, not run time
 117 EOF
 118             return;
 119         }
 120     }
 121
 122     $proc = "Bio::Search::Processor::$algorithm"->new(@_);
 123     return $proc;
 124 }
 125
 126 1;