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://redmine.open-bio.org/projects/bioperl/
  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 use Bio::Root::Version;
  77
  78 =head2 new
  79
  80  Title   : new
  81  Usage   : $proc = Bio::Search::Processor->new -file      => $filename,
  82                                               -algorithm => 'Algorithm' ;
  83  Function: Used to specify and initialize a data processor of search
  84            algorithm results.
  85  Returns : A processor specific to the algorithm type, if it exists.
  86  Args    : -file => filename
  87            -algorithm => algorithm specifier
  88            -fh => filehandle to attach to (file or fh required)
  89
  90 =cut
  91
  92 sub new {
  93
  94     my $type = shift;
  95     my $proc;
  96     my ($module, $load, $algorithm);
  97
  98     my %args = @_;
  99
 100     exists $args{'-algorithm'} or do {
 101         print STDERR "Must supply an algorithm!";
 102         return;
 103     };
 104
 105     $algorithm = $args{'-algorithm'} || $args{'-ALGORITHM'};
 106
 107     $module = "_<Bio/Search/Processor/$algorithm.pm";
 108     $load = "Bio/Search/Processor/$algorithm.pm";
 109
 110     unless ( $main::{$module} ) {
 111         eval { require $load; };
 112         if ( $@ ) {
 113             print STDERR <<"EOF";
 114 $load: $algorithm cannot be found
 115 Exception $@
 116 For more information about the Search/Processor system please see the
 117 Processor docs.  This includes ways of checking for processors at
 118 compile time, not run time
 119 EOF
 120             return;
 121         }
 122     }
 123
 124     $proc = "Bio::Search::Processor::$algorithm"->new(@_);
 125     return $proc;
 126 }
 127
 128 1;