Bio/Search/Processor.pm

   1
   2 #
   3 # BioPerl module for Bio::Search::Processor
   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::Processor - DESCRIPTION of Object
  16
  17 =head1 SYNOPSIS
  18
  19 Give standard usage here
  20
  21 =head1 DESCRIPTION
  22
  23 Describe the object here
  24
  25 =head1 FEEDBACK
  26
  27 =head2 Mailing Lists
  28
  29 User feedback is an integral part of the evolution of this and other
  30 Bioperl modules. Send your comments and suggestions preferably to one
  31 of the Bioperl mailing lists.  Your participation is much appreciated.
  32
  33   bioperl-l@bioperl.org              - General discussion
  34   http://bio.perl.org/MailList.html  - About the mailing lists
  35
  36 =head2 Reporting Bugs
  37
  38 Report bugs to the Bioperl bug tracking system to help us keep track
  39 the bugs and their resolution.  Bug reports can be submitted via email
  40 or the web:
  41
  42   bioperl-bugs@bio.perl.org
  43   http://bugzilla.bioperl.org/
  44
  45 =head1 AUTHOR - Aaron Mackey
  46
  47 Email amackey@virginia.edu
  48
  49 Describe contact details here
  50
  51 =head1 APPENDIX
  52
  53 The rest of the documentation details each of the object
  54 methods. Internal methods are usually preceded with a _
  55
  56 =cut
  57
  58 # Let the code begin...
  59
  60 package Bio::Search::Processor;
  61
  62 use strict;
  63 use vars qw(@ISA);
  64
  65 =head2 new
  66
  67  Title   : new
  68  Usage   : $proc = new Bio::Search::Processor -file      => $filename,
  69                                               -algorithm => 'Algorithm' ;
  70  Function: Used to specify and initialize a data processor of search
  71            algorithm results.
  72  Returns : A processor specific to the algorithm type, if it exists.
  73  Args    : -file => filename
  74            -algorithm => algorithm specifier
  75            -fh => filehandle to attach to (file or fh required)
  76
  77 =cut
  78
  79 sub new {
  80
  81     my $type = shift;
  82     my $proc;
  83     my ($module, $load, $algorithm);
  84
  85     my %args = @_;
  86
  87     exists $args{'-algorithm'} or do {
  88         print STDERR "Must supply an algorithm!";
  89         return undef;
  90     };
  91
  92     $algorithm = $args{'-algorithm'} || $args{'-ALGORITHM'};
  93
  94     $module = "_<Bio/Search/Processor/$algorithm.pm";
  95     $load = "Bio/Search/Processor/$algorithm.pm";
  96
  97     unless ( $main::{$module} ) {
  98         eval { require $load; };
  99         if ( $@ ) {
 100             print STDERR <<"EOF";
 101 $load: $algorithm cannot be found
 102 Exception $@
 103 For more information about the Search/Processor system please see the
 104 Processor docs.  This includes ways of checking for processors at
 105 compile time, not run time
 106 EOF
 107             return undef;
 108         }
 109     }
 110
 111     $proc = "Bio::Search::Processor::$algorithm"->new(@_);
 112     return $proc;
 113 }
 114
 115 1;